From 6bc132acac3676866401add2138f0c1bddda448e Mon Sep 17 00:00:00 2001
From: Melissa Linkert <melissa@glencoesoftware.com>
Date: Fri, 12 Apr 2024 16:45:55 -0500
Subject: [PATCH 1/3] Fix Java 9+ warnings in formats-gpl component

---
 .../src/loci/formats/in/AIMReader.java        |  13 +-
 .../src/loci/formats/in/AliconaReader.java    |   7 +-
 .../src/loci/formats/in/BDReader.java         |  12 +-
 .../src/loci/formats/in/BaseZeissReader.java  |  34 +--
 .../src/loci/formats/in/BioRadReader.java     |  21 +-
 .../src/loci/formats/in/BioRadSCNReader.java  |  19 +-
 .../src/loci/formats/in/BrukerReader.java     |   4 +-
 .../src/loci/formats/in/CellSensReader.java   |  44 ++--
 .../src/loci/formats/in/CellWorxReader.java   |  22 +-
 .../src/loci/formats/in/ColumbusReader.java   |  22 +-
 .../loci/formats/in/DeltavisionReader.java    |  24 +-
 .../src/loci/formats/in/Ecat7Reader.java      |   6 +-
 .../src/loci/formats/in/FEITiffReader.java    |  17 +-
 .../src/loci/formats/in/FV1000Reader.java     |   4 +-
 .../src/loci/formats/in/FlexReader.java       |  16 +-
 .../src/loci/formats/in/FluoviewReader.java   |  21 +-
 .../src/loci/formats/in/GatanDM2Reader.java   |   5 +-
 .../src/loci/formats/in/GelReader.java        |   2 +-
 .../src/loci/formats/in/HRDGDFReader.java     |  10 +-
 .../loci/formats/in/HamamatsuVMSReader.java   |  11 +-
 .../src/loci/formats/in/HitachiReader.java    |   4 +-
 .../src/loci/formats/in/IMODReader.java       |  11 +-
 .../src/loci/formats/in/INRReader.java        |   7 +-
 .../src/loci/formats/in/IPLabReader.java      |  14 +-
 .../src/loci/formats/in/IPWReader.java        |   2 +-
 .../src/loci/formats/in/ImarisHDFReader.java  |  12 +-
 .../src/loci/formats/in/ImarisTiffReader.java |   5 +-
 .../src/loci/formats/in/InCellReader.java     |  16 +-
 .../src/loci/formats/in/InveonReader.java     |  15 +-
 .../src/loci/formats/in/IvisionReader.java    |  11 +-
 .../src/loci/formats/in/KodakReader.java      |  11 +-
 .../src/loci/formats/in/L2DReader.java        |   2 +-
 .../src/loci/formats/in/LIFReader.java        |   2 +-
 .../src/loci/formats/in/LeicaHandler.java     |  53 ++--
 .../src/loci/formats/in/LeicaReader.java      |  16 +-
 .../src/loci/formats/in/LeicaSCNReader.java   |   7 +-
 .../src/loci/formats/in/LiFlimReader.java     |  10 +-
 .../src/loci/formats/in/MIASReader.java       |  10 +-
 .../src/loci/formats/in/MetamorphHandler.java |   2 +-
 .../src/loci/formats/in/MetamorphReader.java  |   8 +-
 .../src/loci/formats/in/MicroCTReader.java    |   4 +-
 .../src/loci/formats/in/ND2Handler.java       |  13 +-
 .../src/loci/formats/in/ND2Reader.java        |   6 +-
 .../src/loci/formats/in/NDPIReader.java       |   2 +-
 .../src/loci/formats/in/NiftiReader.java      |   8 +-
 .../src/loci/formats/in/NikonTiffReader.java  |  13 +-
 .../src/loci/formats/in/OIRReader.java        |   4 +-
 .../loci/formats/in/OlympusTileReader.java    |   4 +-
 .../src/loci/formats/in/OpenlabReader.java    |   9 +-
 .../src/loci/formats/in/OperettaReader.java   |   1 +
 .../src/loci/formats/in/PCORAWReader.java     |   2 +-
 .../src/loci/formats/in/PDSReader.java        |   4 +-
 .../loci/formats/in/PerkinElmerReader.java    |   8 +-
 .../src/loci/formats/in/PrairieMetadata.java  |   6 +-
 .../src/loci/formats/in/PrairieReader.java    |   6 +-
 .../src/loci/formats/in/SBIGReader.java       |  10 +-
 .../src/loci/formats/in/SDTInfo.java          | 236 +++++++++---------
 .../src/loci/formats/in/SVSReader.java        |   6 +-
 .../src/loci/formats/in/ScanrReader.java      |  12 +-
 .../loci/formats/in/SimplePCITiffReader.java  |   5 +-
 .../loci/formats/in/SlidebookTiffReader.java  |   5 +-
 .../src/loci/formats/in/SpiderReader.java     |   2 +-
 .../src/loci/formats/in/TCSReader.java        |   2 +-
 .../src/loci/formats/in/ZeissCZIReader.java   | 125 +++++-----
 .../src/loci/formats/in/ZeissLSMReader.java   |  10 +-
 65 files changed, 547 insertions(+), 488 deletions(-)

diff --git a/components/formats-gpl/src/loci/formats/in/AIMReader.java b/components/formats-gpl/src/loci/formats/in/AIMReader.java
index d40c79bdb66..7f291eebc2b 100644
--- a/components/formats-gpl/src/loci/formats/in/AIMReader.java
+++ b/components/formats-gpl/src/loci/formats/in/AIMReader.java
@@ -27,6 +27,7 @@
 
 import java.io.IOException;
 
+import loci.common.DataTools;
 import loci.common.DateTools;
 import loci.common.RandomAccessInputStream;
 import loci.formats.CoreMetadata;
@@ -152,13 +153,13 @@ else if (key.equals("Orig-ISQ-Dim-p")) {
             token = token.trim();
             if (token.length() > 0) {
               if (xSize == null) {
-                xSize = new Double(token);
+                xSize = DataTools.parseDouble(token);
               }
               else if (ySize == null) {
-                ySize = new Double(token);
+                ySize = DataTools.parseDouble(token);
               }
               else if (zSize == null) {
-                zSize = new Double(token);
+                zSize = DataTools.parseDouble(token);
               }
             }
           }
@@ -169,13 +170,13 @@ else if (key.equals("Orig-ISQ-Dim-um")) {
             token = token.trim();
             if (token.length() > 0) {
               if (xLength == null) {
-                xLength = new Double(token);
+                xLength = DataTools.parseDouble(token);
               }
               else if (yLength == null) {
-                yLength = new Double(token);
+                yLength = DataTools.parseDouble(token);
               }
               else if (zLength == null) {
-                zLength = new Double(token);
+                zLength = DataTools.parseDouble(token);
               }
             }
           }
diff --git a/components/formats-gpl/src/loci/formats/in/AliconaReader.java b/components/formats-gpl/src/loci/formats/in/AliconaReader.java
index fffe5538280..fa9f85129bb 100644
--- a/components/formats-gpl/src/loci/formats/in/AliconaReader.java
+++ b/components/formats-gpl/src/loci/formats/in/AliconaReader.java
@@ -27,6 +27,7 @@
 
 import java.io.IOException;
 
+import loci.common.DataTools;
 import loci.common.RandomAccessInputStream;
 import loci.formats.CoreMetadata;
 import loci.formats.FormatException;
@@ -238,7 +239,7 @@ else if (key.equals("DepthImageOffset")) {
       // used when the dataset was acquired, i.e. detector settings.
       if (voltage != null) {
         store.setDetectorSettingsVoltage(
-                new ElectricPotential(new Double(voltage), UNITS.VOLT), 0, 0);
+                new ElectricPotential(DataTools.parseDouble(voltage), UNITS.VOLT), 0, 0);
 
         // link DetectorSettings to an actual Detector
         String detectorID = MetadataTools.createLSID("Detector", 0, 0);
@@ -253,11 +254,11 @@ else if (key.equals("DepthImageOffset")) {
 
       if (magnification != null) {
         store.setObjectiveCalibratedMagnification(
-          new Double(magnification), 0, 0);
+          DataTools.parseDouble(magnification), 0, 0);
       }
 
       if (workingDistance != null) {
-        store.setObjectiveWorkingDistance(new Length(new Double(workingDistance), UNITS.MICROMETER), 0, 0);
+        store.setObjectiveWorkingDistance(new Length(DataTools.parseDouble(workingDistance), UNITS.MICROMETER), 0, 0);
       }
 
       store.setObjectiveCorrection(MetadataTools.getCorrection("Other"), 0, 0);
diff --git a/components/formats-gpl/src/loci/formats/in/BDReader.java b/components/formats-gpl/src/loci/formats/in/BDReader.java
index 0d40fede37e..75a529c11d1 100644
--- a/components/formats-gpl/src/loci/formats/in/BDReader.java
+++ b/components/formats-gpl/src/loci/formats/in/BDReader.java
@@ -460,11 +460,11 @@ protected void initFile(String id) throws FormatException, IOException {
           }
         }
 
-        Double magnification = new Double(mag);
+        Double magnification = DataTools.parseDouble(mag);
         store.setObjectiveNominalMagnification(magnification, 0, 0);
         if (na != null) {
           na = na.substring(0, 1) + "." + na.substring(1);
-          store.setObjectiveLensNA(new Double(na), 0, 0);
+          store.setObjectiveLensNA(DataTools.parseDouble(na), 0, 0);
         }
         if (naIndex + 1 < tokens.length) {
           store.setObjectiveManufacturer(tokens[naIndex + 1], 0, 0);
@@ -762,10 +762,10 @@ private void parseROIs(MetadataStore store) throws IOException {
       if (cols[2].trim().length() > 0) {
         String rectangleID = MetadataTools.createLSID("Shape", i - firstRow, 0);
         store.setRectangleID(rectangleID, i - firstRow, 0);
-        store.setRectangleX(new Double(cols[2]), i - firstRow, 0);
-        store.setRectangleY(new Double(cols[3]), i - firstRow, 0);
-        store.setRectangleWidth(new Double(cols[4]), i - firstRow, 0);
-        store.setRectangleHeight(new Double(cols[5]), i - firstRow, 0);
+        store.setRectangleX(DataTools.parseDouble(cols[2]), i - firstRow, 0);
+        store.setRectangleY(DataTools.parseDouble(cols[3]), i - firstRow, 0);
+        store.setRectangleWidth(DataTools.parseDouble(cols[4]), i - firstRow, 0);
+        store.setRectangleHeight(DataTools.parseDouble(cols[5]), i - firstRow, 0);
         String roiID = MetadataTools.createLSID("ROI", i - firstRow);
         store.setROIID(roiID, i - firstRow);
         for (int s=0; s<getSeriesCount(); s++) {
diff --git a/components/formats-gpl/src/loci/formats/in/BaseZeissReader.java b/components/formats-gpl/src/loci/formats/in/BaseZeissReader.java
index f69f9d9117f..4e116091e1b 100644
--- a/components/formats-gpl/src/loci/formats/in/BaseZeissReader.java
+++ b/components/formats-gpl/src/loci/formats/in/BaseZeissReader.java
@@ -36,6 +36,7 @@
 import java.util.ArrayList;
 import java.lang.Math;
 
+import loci.common.DataTools;
 import loci.common.DateTools;
 import loci.formats.CoreMetadata;
 import loci.formats.FormatTools;
@@ -400,10 +401,12 @@ protected void fillMetadataPass7(MetadataStore store) throws FormatException, IO
             exposure = exposureTime.values().iterator().next();
           }
           Double exp = 0d;
-          try { exp = new Double(exposure); }
+          try { exp = DataTools.parseDouble(exposure); }
           catch (NumberFormatException e) { }
           catch (NullPointerException e) { }
-          store.setPlaneExposureTime(new Time(exp, UNITS.SECOND), i, plane);
+          if (exp != null) {
+            store.setPlaneExposureTime(new Time(exp, UNITS.SECOND), i, plane);
+          }
 
           int posIndex = i * getImageCount() + plane;
 
@@ -844,12 +847,13 @@ else if (key.equals("ImageHeight")) {
         }
 
         if (key.startsWith("ImageTile") && !(store instanceof DummyMetadata)) {
-          if (!tiles.containsKey(new Integer(value))) {
-            tiles.put(Integer.valueOf(value), 1);
+          Integer intValue = Integer.parseInt(value);
+          if (!tiles.containsKey(intValue)) {
+            tiles.put(intValue, 1);
           }
           else {
-            int v = tiles.get(new Integer(value)).intValue() + 1;
-            tiles.put(new Integer(value), new Integer(v));
+            int v = tiles.get(intValue).intValue() + 1;
+            tiles.put(intValue, Integer.valueOf(v));
           }
         }
 
@@ -909,7 +913,7 @@ else if (key.startsWith("NumberOfRawImages") && rawCount == 0)
         }
         else if (key.startsWith("Emission Wavelength")) {
           if (cIndex != -1) {
-            Double wave = new Double(value);
+            Double wave = DataTools.parseDouble(value);
             Length emission = FormatTools.getEmissionWavelength(wave);
             if (emission != null) {
               emWavelength.put(cIndex, emission);
@@ -918,7 +922,7 @@ else if (key.startsWith("Emission Wavelength")) {
         }
         else if (key.startsWith("Excitation Wavelength")) {
           if (cIndex != -1) {
-            Double wave = new Double(Double.parseDouble(value));
+            Double wave = DataTools.parseDouble(value);
             Length excitation = FormatTools.getExcitationWavelength(wave);
             if (excitation != null) {
               exWavelength.put(cIndex, excitation);
@@ -931,9 +935,9 @@ else if (key.startsWith("Channel Name")) {
           }
         }
         else if (key.startsWith("Exposure Time [ms]")) {
-          if (exposureTime.get(new Integer(cIndex)) == null) {
+          if (exposureTime.get(Integer.valueOf(cIndex)) == null) {
             double exp = Double.parseDouble(value) / 1000;
-            exposureTime.put(new Integer(cIndex), String.valueOf(exp));
+            exposureTime.put(Integer.valueOf(cIndex), String.valueOf(exp));
           }
         }
         else if (key.startsWith("User Name")) {
@@ -960,7 +964,7 @@ else if (key.startsWith("Objective ID")) {
           store.setObjectiveImmersion(MetadataTools.getImmersion("Other"), 0, 0);
         }
         else if (key.startsWith("Objective N.A.")) {
-          store.setObjectiveLensNA(new Double(value), 0, 0);
+          store.setObjectiveLensNA(DataTools.parseDouble(value), 0, 0);
         }
         else if (key.startsWith("Objective Name")) {
           String[] tokens = value.split(" ");
@@ -971,14 +975,14 @@ else if (key.startsWith("Objective Name")) {
                   Double.parseDouble(tokens[q].substring(0, slash - q));
               String na = tokens[q].substring(slash + 1);
               store.setObjectiveNominalMagnification(mag, 0, 0);
-              store.setObjectiveLensNA(new Double(na), 0, 0);
+              store.setObjectiveLensNA(DataTools.parseDouble(na), 0, 0);
               store.setObjectiveCorrection(MetadataTools.getCorrection(tokens[q - 1]), 0, 0);
               break;
             }
           }
         }
         else if (key.startsWith("Objective Working Distance")) {
-          store.setObjectiveWorkingDistance(new Length(new Double(value), UNITS.MICROMETER), 0, 0);
+          store.setObjectiveWorkingDistance(new Length(DataTools.parseDouble(value), UNITS.MICROMETER), 0, 0);
         }
         else if (key.startsWith("Objective Immersion Type")) {
           String immersion = "Other";
@@ -1004,10 +1008,10 @@ else if (key.startsWith("Stage Position Y")) {
           addGlobalMetaList("Y position for position", value);
         }
         else if (key.startsWith("Orca Analog Gain")) {
-          detectorGain.put(cIndex, new Double(value));
+          detectorGain.put(cIndex, DataTools.parseDouble(value));
         }
         else if (key.startsWith("Orca Analog Offset")) {
-          detectorOffset.put(cIndex, new Double(value));
+          detectorOffset.put(cIndex, DataTools.parseDouble(value));
         }
         else if (key.startsWith("Comments")) {
           imageDescription = value;
diff --git a/components/formats-gpl/src/loci/formats/in/BioRadReader.java b/components/formats-gpl/src/loci/formats/in/BioRadReader.java
index 713e52a338e..8e8089629ae 100644
--- a/components/formats-gpl/src/loci/formats/in/BioRadReader.java
+++ b/components/formats-gpl/src/loci/formats/in/BioRadReader.java
@@ -32,6 +32,7 @@
 import java.util.List;
 import java.util.StringTokenizer;
 
+import loci.common.DataTools;
 import loci.common.Location;
 import loci.common.RandomAccessInputStream;
 import loci.common.xml.BaseHandler;
@@ -502,8 +503,8 @@ else if (list[i].endsWith("data.raw")) {
       store.setObjectiveID(objectiveID, 0, 0);
       store.setObjectiveSettingsID(objectiveID, 0);
 
-      store.setObjectiveLensNA(new Double(lens), 0, 0);
-      store.setObjectiveNominalMagnification(new Double(magFactor), 0, 0);
+      store.setObjectiveLensNA(Double.valueOf(lens), 0, 0);
+      store.setObjectiveNominalMagnification(Double.valueOf(magFactor), 0, 0);
       store.setObjectiveCorrection(MetadataTools.getCorrection("Other"), 0, 0);
       store.setObjectiveImmersion(MetadataTools.getImmersion("Other"), 0, 0);
 
@@ -673,7 +674,7 @@ else if (key.startsWith("SETTING")) {
                         while (nextDetector > offset.size()) {
                           offset.add(null);
                         }
-                        offset.add(new Double(value));
+                        offset.add(DataTools.parseDouble(value));
                       }
                     }
                     else if (key.endsWith("GAIN")) {
@@ -684,7 +685,7 @@ else if (key.endsWith("GAIN")) {
                         while (nextDetector > gain.size()) {
                           gain.add(null);
                         }
-                        gain.add(new Double(value));
+                        gain.add(DataTools.parseDouble(value));
                       }
                     }
                     nextDetector++;
@@ -698,7 +699,7 @@ else if (key.endsWith("GAIN")) {
                     int type = Integer.parseInt(values[0]);
                     if (type == 257 && values.length >= 3) {
                       // found length of axis in um
-                      Double pixelSize = new Double(values[2]);
+                      Double pixelSize = DataTools.parseDouble(values[2]);
                       if (key.equals("AXIS_2")) {
                         Length size =
                           FormatTools.getPhysicalSizeX(pixelSize);
@@ -722,7 +723,7 @@ else if (key.equals("AXIS_3")) {
             }
             else if (n.p.startsWith("AXIS_2")) {
               String[] values = n.p.split(" ");
-              Double pixelSize = new Double(values[3]);
+              Double pixelSize = DataTools.parseDouble(values[3]);
               Length size = FormatTools.getPhysicalSizeX(pixelSize);
               if (size != null) {
                 store.setPixelsPhysicalSizeX(size, 0);
@@ -730,7 +731,7 @@ else if (n.p.startsWith("AXIS_2")) {
             }
             else if (n.p.startsWith("AXIS_3")) {
               String[] values = n.p.split(" ");
-              Double pixelSize = new Double(values[3]);
+              Double pixelSize = DataTools.parseDouble(values[3]);
               Length size = FormatTools.getPhysicalSizeY(pixelSize);
               if (size != null) {
                 store.setPixelsPhysicalSizeY(size, 0);
@@ -754,7 +755,7 @@ else if (n.p.startsWith("AXIS_3")) {
                   Double mag = Double.parseDouble(values[11]);
                   store.setObjectiveNominalMagnification(mag, 0, 0);
 
-                  Double sizeZ = new Double(values[14]);
+                  Double sizeZ = DataTools.parseDouble(values[14]);
                   Length size = FormatTools.getPhysicalSizeZ(sizeZ);
                   if (size != null) {
                     store.setPixelsPhysicalSizeZ(size, 0);
@@ -851,8 +852,8 @@ else if (n.p.startsWith("AXIS_3")) {
                     String detectorID =
                       MetadataTools.createLSID("Detector", 0, i);
                     store.setDetectorID(detectorID, 0, i);
-                    store.setDetectorOffset(new Double(values[i * 3]), 0, i);
-                    store.setDetectorGain(new Double(values[i * 3 + 1]), 0, i);
+                    store.setDetectorOffset(DataTools.parseDouble(values[i * 3]), 0, i);
+                    store.setDetectorGain(DataTools.parseDouble(values[i * 3 + 1]), 0, i);
                     store.setDetectorType(MetadataTools.getDetectorType("Other"), 0, i);
                   }
                   break;
diff --git a/components/formats-gpl/src/loci/formats/in/BioRadSCNReader.java b/components/formats-gpl/src/loci/formats/in/BioRadSCNReader.java
index 2365f8b068c..ea107fb9107 100644
--- a/components/formats-gpl/src/loci/formats/in/BioRadSCNReader.java
+++ b/components/formats-gpl/src/loci/formats/in/BioRadSCNReader.java
@@ -28,6 +28,7 @@
 import java.io.IOException;
 import java.util.ArrayList;
 
+import loci.common.DataTools;
 import loci.common.RandomAccessInputStream;
 import loci.common.xml.BaseHandler;
 import loci.common.xml.XMLTools;
@@ -245,10 +246,10 @@ else if ("channel_count".equals(key)) {
         core.get(0).sizeC = Integer.parseInt(value);
       }
       else if ("application_gain".equals(key)) {
-        gain = new Double(value);
+        gain = DataTools.parseDouble(value);
       }
       else if ("exposure_time".equals(key)) {
-        exposureTime = new Double(value);
+        exposureTime = DataTools.parseDouble(value);
       }
       else if ("name".equals(key)) {
         imageName = value;
@@ -287,12 +288,18 @@ else if (value <= 65535) {
         }
         else if (key.equals("size_mm")) {
           if (attrKey.equals("width")) {
-            physicalSizeX = new Double(attrValue) / getSizeX();
-            physicalSizeX *= 1000; // convert from mm to um
+            Double size = DataTools.parseDouble(attrValue);
+            if (size != null) {
+              physicalSizeX = size / getSizeX();
+              physicalSizeX *= 1000; // convert from mm to um
+            }
           }
           else if (attrKey.equals("height")) {
-            physicalSizeY = new Double(attrValue) / getSizeY();
-            physicalSizeY *= 1000; // convert from mm to um
+            Double size = DataTools.parseDouble(attrValue);
+            if (size != null) {
+              physicalSizeY = size / getSizeY();
+              physicalSizeY *= 1000; // convert from mm to um
+            }
           }
         }
         else if (key.equals("serial_number")) {
diff --git a/components/formats-gpl/src/loci/formats/in/BrukerReader.java b/components/formats-gpl/src/loci/formats/in/BrukerReader.java
index 25b61f669f9..d9d6ba5ec89 100644
--- a/components/formats-gpl/src/loci/formats/in/BrukerReader.java
+++ b/components/formats-gpl/src/loci/formats/in/BrukerReader.java
@@ -216,12 +216,12 @@ protected void initFile(String id) throws FormatException, IOException {
       public int compare(String s1, String s2) {
         Integer i1 = 0;
         try {
-          i1 = new Integer(s1);
+          i1 = Integer.parseInt(s1);
         }
         catch (NumberFormatException e) { }
         Integer i2 = 0;
         try {
-          i2 = new Integer(s2);
+          i2 = Integer.parseInt(s2);
         }
         catch (NumberFormatException e) { }
 
diff --git a/components/formats-gpl/src/loci/formats/in/CellSensReader.java b/components/formats-gpl/src/loci/formats/in/CellSensReader.java
index 0884c9b4767..0abf184a7cb 100644
--- a/components/formats-gpl/src/loci/formats/in/CellSensReader.java
+++ b/components/formats-gpl/src/loci/formats/in/CellSensReader.java
@@ -1746,7 +1746,7 @@ else if (extendedField && (realType == PROPERTY_SET_VOLUME ||
                 value = String.valueOf(vsi.readDouble());
                 break;
               case BOOLEAN:
-                value = new Boolean(vsi.readBoolean()).toString();
+                value = Boolean.valueOf(vsi.readBoolean()).toString();
                 break;
               case TCHAR:
               case UNICODE_TCHAR:
@@ -1884,72 +1884,72 @@ else if (tag == DEVICE_MANUFACTURER) {
                 pyramid.deviceManufacturers.add(value);
               }
               else if (tag == EXPOSURE_TIME && tagPrefix.length() == 0) {
-                pyramid.exposureTimes.add(new Long(value));
+                pyramid.exposureTimes.add(Long.parseLong(value));
               }
               else if (tag == EXPOSURE_TIME) {
-                pyramid.defaultExposureTime = new Long(value);
+                pyramid.defaultExposureTime = Long.parseLong(value);
                 pyramid.otherExposureTimes.add(pyramid.defaultExposureTime);
               }
               else if (tag == CREATION_TIME && pyramid.acquisitionTime == null) {
-                pyramid.acquisitionTime = new Long(value);
+                pyramid.acquisitionTime = Long.parseLong(value);
               }
               else if (tag == REFRACTIVE_INDEX) {
-                pyramid.refractiveIndex = new Double(value);
+                pyramid.refractiveIndex = DataTools.parseDouble(value);
               }
               else if (tag == OBJECTIVE_MAG) {
-                pyramid.magnification = new Double(value);
+                pyramid.magnification = DataTools.parseDouble(value);
               }
               else if (tag == NUMERICAL_APERTURE) {
-                pyramid.numericalAperture = new Double(value);
+                pyramid.numericalAperture = DataTools.parseDouble(value);
               }
               else if (tag == WORKING_DISTANCE) {
-                pyramid.workingDistance = new Double(value);
+                pyramid.workingDistance = DataTools.parseDouble(value);
               }
               else if (tag == OBJECTIVE_NAME) {
                 pyramid.objectiveNames.add(value);
               }
               else if (tag == OBJECTIVE_TYPE) {
-                pyramid.objectiveTypes.add(new Integer(value));
+                pyramid.objectiveTypes.add(Integer.parseInt(value));
               }
               else if (tag == BIT_DEPTH) {
-                pyramid.bitDepth = new Integer(value);
+                pyramid.bitDepth = Integer.parseInt(value);
               }
               else if (tag == X_BINNING) {
-                pyramid.binningX = new Integer(value);
+                pyramid.binningX = Integer.parseInt(value);
               }
               else if (tag == Y_BINNING) {
-                pyramid.binningY = new Integer(value);
+                pyramid.binningY = Integer.parseInt(value);
               }
               else if (tag == CAMERA_GAIN) {
-                pyramid.gain = new Double(value);
+                pyramid.gain = DataTools.parseDouble(value);
               }
               else if (tag == CAMERA_OFFSET) {
-                pyramid.offset = new Double(value);
+                pyramid.offset = DataTools.parseDouble(value);
               }
               else if (tag == RED_GAIN) {
-                pyramid.redGain = new Double(value);
+                pyramid.redGain = DataTools.parseDouble(value);
               }
               else if (tag == GREEN_GAIN) {
-                pyramid.greenGain = new Double(value);
+                pyramid.greenGain = DataTools.parseDouble(value);
               }
               else if (tag == BLUE_GAIN) {
-                pyramid.blueGain = new Double(value);
+                pyramid.blueGain = DataTools.parseDouble(value);
               }
               else if (tag == RED_OFFSET) {
-                pyramid.redOffset = new Double(value);
+                pyramid.redOffset = DataTools.parseDouble(value);
               }
               else if (tag == GREEN_OFFSET) {
-                pyramid.greenOffset = new Double(value);
+                pyramid.greenOffset = DataTools.parseDouble(value);
               }
               else if (tag == BLUE_OFFSET) {
-                pyramid.blueOffset = new Double(value);
+                pyramid.blueOffset = DataTools.parseDouble(value);
               }
               else if (tag == VALUE) {
                 if (tagPrefix.equals("Channel Wavelength ")) {
-                  pyramid.channelWavelengths.add(new Double(value));
+                  pyramid.channelWavelengths.add(DataTools.parseDouble(value));
                 }
                 else if (tagPrefix.startsWith("Objective Working Distance")) {
-                  pyramid.workingDistance = new Double(value);
+                  pyramid.workingDistance = DataTools.parseDouble(value);
                 }
                 else if (tagPrefix.equals("Z start position")) {
                   pyramid.zStart = DataTools.parseDouble(value);
diff --git a/components/formats-gpl/src/loci/formats/in/CellWorxReader.java b/components/formats-gpl/src/loci/formats/in/CellWorxReader.java
index 244c81add99..1cd3593464d 100644
--- a/components/formats-gpl/src/loci/formats/in/CellWorxReader.java
+++ b/components/formats-gpl/src/loci/formats/in/CellWorxReader.java
@@ -149,7 +149,7 @@ else if (key.startsWith("WellsSelection")) {
             int row = Integer.parseInt(key.substring(14)) - 1;
             String[] mapping = value.split(",");
             for (int col=0; col<xWells; col++) {
-              if (new Boolean(mapping[col].trim()).booleanValue()) {
+              if (Boolean.parseBoolean(mapping[col].trim())) {
                 String base = plate + FormatTools.getWellName(row, col);
                 Location pnl = new Location(base + ".pnl");
                 if (pnl.exists()) {
@@ -600,7 +600,7 @@ else if (key.startsWith("WellsSelection")) {
         int row = Integer.parseInt(key.substring(14)) - 1;
         String[] mapping = value.split(",");
         for (int col=0; col<xWells; col++) {
-          if (new Boolean(mapping[col].trim()).booleanValue()) {
+          if (Boolean.parseBoolean(mapping[col].trim())) {
             wellFiles[row][col] = new String[1];
           }
         }
@@ -633,11 +633,11 @@ else if (key.startsWith("SiteSelection")) {
         int row = Integer.parseInt(key.substring(13)) - 1;
         String[] mapping = value.split(",");
         for (int col=0; col<xFields; col++) {
-          fieldMap[row][col] = new Boolean(mapping[col].trim()).booleanValue();
+          fieldMap[row][col] = Boolean.parseBoolean(mapping[col].trim());
         }
       }
       else if (key.equals("Waves")) {
-        doChannels = new Boolean(value.toLowerCase());
+        doChannels = Boolean.parseBoolean(value.toLowerCase());
       }
       else if (key.equals("NWavelengths")) {
         wavelengths = new String[Integer.parseInt(value)];
@@ -778,8 +778,8 @@ protected void parseWellLogFile(int wellIndex, MetadataStore store)
       }
       else if (key.equals("Scan Origin")) {
         String[] axes = value.split(",");
-        Double posX = new Double(axes[0]);
-        Double posY = new Double(axes[1]);
+        Double posX = DataTools.parseDouble(axes[0]);
+        Double posY = DataTools.parseDouble(axes[1]);
         for (int fieldRow=0; fieldRow<fieldMap.length; fieldRow++) {
           for (int fieldCol=0; fieldCol<fieldMap[fieldRow].length; fieldCol++) {
             if (fieldMap[fieldRow][fieldCol] && wellFiles[row][col] != null) {
@@ -799,8 +799,8 @@ else if (key.equals("Scan Area")) {
         int s = value.indexOf('x');
         if (s > 0) {
           int end = value.indexOf(" ", s + 2);
-          Double xSize = new Double(value.substring(0, s).trim());
-          Double ySize = new Double(value.substring(s + 1, end).trim());
+          Double xSize = DataTools.parseDouble(value.substring(0, s).trim());
+          Double ySize = DataTools.parseDouble(value.substring(s + 1, end).trim());
 
           Length x = FormatTools.getPhysicalSizeX(xSize / getSizeX());
           Length y = FormatTools.getPhysicalSizeY(ySize / getSizeY());
@@ -827,7 +827,7 @@ else if (key.startsWith("Channel")) {
           token = token.trim();
           if (token.startsWith("gain")) {
             String instrumentID = MetadataTools.createLSID("Instrument", 0);
-            Double gain = new Double(token.replaceAll("gain ", ""));
+            Double gain = DataTools.parseDouble(token.replaceAll("gain ", ""));
             String detectorID = MetadataTools.createLSID("Detector", 0, 0);
 
             store.setInstrumentID(instrumentID, 0);
@@ -854,8 +854,8 @@ else if (token.startsWith("EX")) {
                 }
               }
 
-              Double emission = new Double(em);
-              Double excitation = new Double(ex);
+              Double emission = DataTools.parseDouble(em);
+              Double excitation = DataTools.parseDouble(ex);
 
               Length exWave = FormatTools.getExcitationWavelength(excitation);
               Length emWave = FormatTools.getEmissionWavelength(emission);
diff --git a/components/formats-gpl/src/loci/formats/in/ColumbusReader.java b/components/formats-gpl/src/loci/formats/in/ColumbusReader.java
index fcf52845653..ff22e824c02 100644
--- a/components/formats-gpl/src/loci/formats/in/ColumbusReader.java
+++ b/components/formats-gpl/src/loci/formats/in/ColumbusReader.java
@@ -536,7 +536,7 @@ else if (name.equals("ChannelName")) {
           p.channelName = value;
         }
         else if (name.equals("ChannelColor")) {
-          Long color = new Long(value);
+          Long color = Long.parseLong(value);
           int blue = (int) ((color >> 24) & 0xff);
           int green = (int) ((color >> 16) & 0xff);
           int red = (int) ((color >> 8) & 0xff);
@@ -548,36 +548,36 @@ else if (name.equals("ChannelColor")) {
           //p.channelColor = new Color(red, green, blue, alpha);
         }
         else if (name.equals("MeasurementTimeOffset")) {
-          p.deltaT = new Double(value);
+          p.deltaT = DataTools.parseDouble(value);
         }
         else if (name.equals("AbsTime")) {
           p.deltaT = new Timestamp(value).asInstant().getMillis() / 1000d;
         }
         else if (name.equals("MainEmissionWavelength")) {
-          p.emWavelength = new Double(value);
+          p.emWavelength = DataTools.parseDouble(value);
         }
         else if (name.equals("MainExcitationWavelength")) {
-          p.exWavelength = new Double(value);
+          p.exWavelength = DataTools.parseDouble(value);
         }
         else if (name.equals("ImageResolutionX")) {
           String unit = attrs.getNamedItem("Unit").getNodeValue();
-          p.sizeX = correctUnits(new Double(value), unit);
+          p.sizeX = correctUnits(DataTools.parseDouble(value), unit);
         }
         else if (name.equals("ImageResolutionY")) {
           String unit = attrs.getNamedItem("Unit").getNodeValue();
-          p.sizeY = correctUnits(new Double(value), unit);
+          p.sizeY = correctUnits(DataTools.parseDouble(value), unit);
         }
         else if (name.equals("PositionX")) {
           String unit = attrs.getNamedItem("Unit").getNodeValue();
-          p.positionX = correctUnits(new Double(value), unit);
+          p.positionX = correctUnits(DataTools.parseDouble(value), unit);
         }
         else if (name.equals("PositionY")) {
           String unit = attrs.getNamedItem("Unit").getNodeValue();
-          p.positionY = correctUnits(new Double(value), unit);
+          p.positionY = correctUnits(DataTools.parseDouble(value), unit);
         }
         else if (name.equals("PositionZ")) {
           String unit = attrs.getNamedItem("Unit").getNodeValue();
-          p.positionZ = correctUnits(new Double(value), unit);
+          p.positionZ = correctUnits(DataTools.parseDouble(value), unit);
         }
       }
 
@@ -725,10 +725,10 @@ else if (currentName.equals("Reference")) {
         metadataFiles.add(new Location(value).toString());
       }
       else if (currentName.equals("PlateRows")) {
-        plateRows = new Integer(value);
+        plateRows = Integer.parseInt(value);
       }
       else if (currentName.equals("PlateColumns")) {
-        plateColumns = new Integer(value);
+        plateColumns = Integer.parseInt(value);
       }
 
       currentName = null;
diff --git a/components/formats-gpl/src/loci/formats/in/DeltavisionReader.java b/components/formats-gpl/src/loci/formats/in/DeltavisionReader.java
index f3cc590d4d1..4d415a6f837 100644
--- a/components/formats-gpl/src/loci/formats/in/DeltavisionReader.java
+++ b/components/formats-gpl/src/loci/formats/in/DeltavisionReader.java
@@ -859,17 +859,17 @@ protected void initExtraMetadata() throws FormatException, IOException {
         }
       }
 
-      Double x = new Double(pixX);
+      Double x = Double.valueOf(pixX);
       Length sizeX = FormatTools.getPhysicalSizeX(x);
       if (sizeX != null) {
         store.setPixelsPhysicalSizeX(sizeX, series);
       }
-      Double y = new Double(pixY);
+      Double y = Double.valueOf(pixY);
       Length sizeY = FormatTools.getPhysicalSizeY(y);
       if (sizeY != null) {
         store.setPixelsPhysicalSizeY(sizeY, series);
       }
-      Double z = new Double(pixZ);
+      Double z = Double.valueOf(pixZ);
       Length sizeZ = FormatTools.getPhysicalSizeZ(z);
       if (sizeZ != null) {
         store.setPixelsPhysicalSizeZ(sizeZ, series);
@@ -948,12 +948,12 @@ else if (backwardsStageY && xTiles == 1) {
 
         DVExtHdrFields hdr = extHdrFields[getPlaneIndex(seriesIndex, i)];
         if (expTime[coords[1]] == null) {
-          expTime[coords[1]] = new Double(hdr.expTime);
+          expTime[coords[1]] = Double.valueOf(hdr.expTime);
         }
 
         // plane timing
         store.setPlaneDeltaT(
-          new Time(new Double(hdr.timeStampSeconds), UNITS.SECOND), series, i);
+          new Time(Double.valueOf(hdr.timeStampSeconds), UNITS.SECOND), series, i);
         store.setPlaneExposureTime(new Time(expTime[coords[1]], UNITS.SECOND), series, i);
 
         // stage position
@@ -967,9 +967,9 @@ else if (backwardsStageY && xTiles == 1) {
           int w = coords[1];
 
           Length emission =
-            FormatTools.getEmissionWavelength(new Double(waves[w]));
+            FormatTools.getEmissionWavelength(Double.valueOf(waves[w]));
           Length excitation =
-            FormatTools.getExcitationWavelength(new Double(hdr.exWavelen));
+            FormatTools.getExcitationWavelength(Double.valueOf(hdr.exWavelen));
 
           if (emission != null) {
             store.setChannelEmissionWavelength(emission, series, w);
@@ -977,7 +977,7 @@ else if (backwardsStageY && xTiles == 1) {
           if (excitation != null) {
             store.setChannelExcitationWavelength(excitation, series, w);
           }
-          if (ndFilters[w] == null) ndFilters[w] = new Double(hdr.ndFilter);
+          if (ndFilters[w] == null) ndFilters[w] = Double.valueOf(hdr.ndFilter);
           store.setChannelNDFilter(ndFilters[w], series, w);
         }
       }
@@ -1262,14 +1262,14 @@ private boolean parseLogFile(MetadataStore store)
             }
 
             try {
-              Double mag = new Double(magnification);
+              Double mag = DataTools.parseDouble(magnification);
               store.setObjectiveNominalMagnification(mag, 0, 0);
             }
             catch (NumberFormatException e) {
               LOGGER.warn("Could not parse magnification '{}'", magnification);
             }
             try {
-              store.setObjectiveLensNA(new Double(na), 0, 0);
+              store.setObjectiveLensNA(DataTools.parseDouble(na), 0, 0);
             }
             catch (NumberFormatException e) {
               LOGGER.warn("Could not parse N.A. '{}'", na);
@@ -1308,7 +1308,7 @@ else if (key.equals("Pixel Size")) {
           for (int q=0; q<pixelSizes.length; q++) {
             Double size = null;
             try {
-              size = new Double(pixelSizes[q].trim());
+              size = DataTools.parseDouble(pixelSizes[q].trim());
             }
             catch (NumberFormatException e) {
               LOGGER.warn("Could not parse pixel size '{}'",
@@ -1364,7 +1364,7 @@ else if (key.equals("Gain")) {
             store.setDetectorID(detectorID, 0, 0);
             for (int series=0; series<getSeriesCount(); series++) {
               for (int c=0; c<getSizeC(); c++) {
-                store.setDetectorSettingsGain(new Double(value), series, c);
+                store.setDetectorSettingsGain(DataTools.parseDouble(value), series, c);
                 store.setDetectorSettingsID(detectorID, series, c);
               }
             }
diff --git a/components/formats-gpl/src/loci/formats/in/Ecat7Reader.java b/components/formats-gpl/src/loci/formats/in/Ecat7Reader.java
index adc0fffd9b3..f214bd1fe4b 100644
--- a/components/formats-gpl/src/loci/formats/in/Ecat7Reader.java
+++ b/components/formats-gpl/src/loci/formats/in/Ecat7Reader.java
@@ -381,11 +381,11 @@ protected void initFile(String id) throws FormatException, IOException {
     if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
       store.setImageDescription(description, 0);
       Length sizeX =
-        FormatTools.getPhysicalSizeX(new Double(xPixelSize));
+        FormatTools.getPhysicalSizeX(Double.valueOf(xPixelSize));
       Length sizeY =
-        FormatTools.getPhysicalSizeY(new Double(yPixelSize));
+        FormatTools.getPhysicalSizeY(Double.valueOf(yPixelSize));
       Length sizeZ =
-        FormatTools.getPhysicalSizeZ(new Double(zPixelSize));
+        FormatTools.getPhysicalSizeZ(Double.valueOf(zPixelSize));
 
       if (sizeX != null) {
         store.setPixelsPhysicalSizeX(sizeX, 0);
diff --git a/components/formats-gpl/src/loci/formats/in/FEITiffReader.java b/components/formats-gpl/src/loci/formats/in/FEITiffReader.java
index ecba6d8549f..b9b796509bc 100644
--- a/components/formats-gpl/src/loci/formats/in/FEITiffReader.java
+++ b/components/formats-gpl/src/loci/formats/in/FEITiffReader.java
@@ -33,6 +33,7 @@
 import java.util.Deque;
 import java.util.HashMap;
 
+import loci.common.DataTools;
 import loci.common.DateTools;
 import loci.common.IniList;
 import loci.common.IniParser;
@@ -227,9 +228,9 @@ else if (stageTable != null) {
 
           IniTable scanTable = ini.getTable("Scan");
  
-          sizeX = new Double(scanTable.get("PixelWidth"));
-          sizeY = new Double(scanTable.get("PixelHeight"));
-          timeIncrement = new Double(scanTable.get("FrameTime"));
+          sizeX = DataTools.parseDouble(scanTable.get("PixelWidth"));
+          sizeY = DataTools.parseDouble(scanTable.get("PixelHeight"));
+          timeIncrement = DataTools.parseDouble(scanTable.get("FrameTime"));
         }
       }
       else {
@@ -238,8 +239,8 @@ else if (stageTable != null) {
         imageDescription = dataTable.get("szUserText");
 
         String magnification = ini.getTable("Vector").get("Magnification");
-        sizeX = new Double(magnification) * MAG_MULTIPLIER;
-        sizeY = new Double(magnification) * MAG_MULTIPLIER;
+        sizeX = DataTools.parseDouble(magnification) * MAG_MULTIPLIER;
+        sizeY = DataTools.parseDouble(magnification) * MAG_MULTIPLIER;
 
         IniTable scanTable = ini.getTable("Vector.Sysscan");
         final Double posX = Double.valueOf(scanTable.get("PositionX"));
@@ -421,18 +422,18 @@ else if (key.equals("User")) {
           userName = value;
         }
         else if (key.equals("Magnification")) {
-          magnification = new Double(value);
+          magnification = DataTools.parseDouble(value);
         }
 
         else if ((key.endsWith("X") && "PixelSize".equals(parent)) ||
           (key.endsWith(" pixelWidth") && "FeiImage".equals(parent)))
         {
-          sizeX = new Double(value);
+          sizeX = DataTools.parseDouble(value);
         }
         else if ((key.endsWith("Y") && "PixelSize".equals(parent)) ||
           (key.endsWith(" pixelHeight") && "FeiImage".equals(parent)))
         {
-          sizeY = new Double(value);
+          sizeY = DataTools.parseDouble(value);
         }
       }
     }
diff --git a/components/formats-gpl/src/loci/formats/in/FV1000Reader.java b/components/formats-gpl/src/loci/formats/in/FV1000Reader.java
index e80b248f1a7..f6b5fb758a2 100644
--- a/components/formats-gpl/src/loci/formats/in/FV1000Reader.java
+++ b/components/formats-gpl/src/loci/formats/in/FV1000Reader.java
@@ -444,13 +444,13 @@ protected void initFile(String id) throws FormatException, IOException {
       if (key.startsWith("IniFileName") && key.indexOf("Thumb") == -1 &&
         !isPreviewName(value))
       {
-        filenames.put(new Integer(key.substring(11)), value);
+        filenames.put(Integer.parseInt(key.substring(11)), value);
       }
       else if (key.startsWith("RoiFileName") && key.indexOf("Thumb") == -1 &&
         !isPreviewName(value))
       {
         try {
-          roiFilenames.put(new Integer(key.substring(11)), value);
+          roiFilenames.put(Integer.parseInt(key.substring(11)), value);
         }
         catch (NumberFormatException e) { }
       }
diff --git a/components/formats-gpl/src/loci/formats/in/FlexReader.java b/components/formats-gpl/src/loci/formats/in/FlexReader.java
index 56724742002..01c9f06de9c 100644
--- a/components/formats-gpl/src/loci/formats/in/FlexReader.java
+++ b/components/formats-gpl/src/loci/formats/in/FlexReader.java
@@ -1552,7 +1552,7 @@ else if (qName.equals("Barcode")) {
       else if (qName.equals("Wavelength") && populateCore) {
         String lsid = MetadataTools.createLSID("LightSource", 0, nextLaser);
         store.setLaserID(lsid, 0, nextLaser);
-        Double wavelength = new Double(value);
+        Double wavelength = DataTools.parseDouble(value);
         Length wave = FormatTools.getWavelength(wavelength);
         if (wave != null) {
           store.setLaserWavelength(wave, 0, nextLaser);
@@ -1566,11 +1566,11 @@ else if (qName.equals("Wavelength") && populateCore) {
         }
       }
       else if (qName.equals("Magnification") && populateCore) {
-        store.setObjectiveCalibratedMagnification(new Double(value), 0,
+        store.setObjectiveCalibratedMagnification(DataTools.parseDouble(value), 0,
           nextObjective);
       }
       else if (qName.equals("NumAperture") && populateCore) {
-        store.setObjectiveLensNA(new Double(value), 0, nextObjective);
+        store.setObjectiveLensNA(DataTools.parseDouble(value), 0, nextObjective);
       }
       else if (qName.equals("Immersion") && populateCore) {
         String immersion = "Other";
@@ -1586,7 +1586,7 @@ else if (qName.equals("Immersion") && populateCore) {
         }
       }
       else if (qName.equals("OffsetX") || qName.equals("OffsetY")) {
-        Double offset = new Double(Double.parseDouble(value) * 1000000);
+        Double offset = Double.valueOf(Double.parseDouble(value) * 1000000);
         if (qName.equals("OffsetX")) xPositions.add(offset);
         else yPositions.add(offset);
       }
@@ -1628,11 +1628,11 @@ else if (qName.equals("CameraRef")) {
         }
         else if (qName.equals("ImageResolutionX")) {
           double v = Double.parseDouble(value) * 1000000;
-          xSizes.add(new Double(v));
+          xSizes.add(Double.valueOf(v));
         }
         else if (qName.equals("ImageResolutionY")) {
           double v = Double.parseDouble(value) * 1000000;
-          ySizes.add(new Double(v));
+          ySizes.add(Double.valueOf(v));
         }
         else if (qName.equals("PositionX")) {
           final double v = Double.parseDouble(value) * 1000000;
@@ -1656,10 +1656,10 @@ else if (qName.equals("PositionZ")) {
           }
         }
         else if (qName.equals("TimepointOffsetUsed")) {
-          planeDeltaT.add(new Double(value));
+          planeDeltaT.add(DataTools.parseDouble(value));
         }
         else if (qName.equals("CameraExposureTime")) {
-          planeExposureTime.add(new Double(value));
+          planeExposureTime.add(DataTools.parseDouble(value));
         }
         else if (qName.equals("LightSourceCombinationRef")) {
           lightSourceCombinationRefs.add(value);
diff --git a/components/formats-gpl/src/loci/formats/in/FluoviewReader.java b/components/formats-gpl/src/loci/formats/in/FluoviewReader.java
index 52145e5c44c..774304fe2f2 100644
--- a/components/formats-gpl/src/loci/formats/in/FluoviewReader.java
+++ b/components/formats-gpl/src/loci/formats/in/FluoviewReader.java
@@ -31,6 +31,7 @@
 import java.math.RoundingMode;
 import java.util.ArrayList;
 
+import loci.common.DataTools;
 import loci.common.DateTools;
 import loci.common.RandomAccessInputStream;
 import loci.formats.CoreMetadata;
@@ -142,8 +143,8 @@ public boolean isThisType(RandomAccessInputStream stream) throws IOException {
     String com = ifd.getComment();
     if (com == null) com = "";
     return (com.indexOf(FLUOVIEW_MAGIC_STRING) != -1 &&
-      ifd.containsKey(new Integer(MMHEADER)) ||
-      ifd.containsKey(new Integer(MMSTAMP))) ||
+      ifd.containsKey(Integer.valueOf(MMHEADER)) ||
+      ifd.containsKey(Integer.valueOf(MMSTAMP))) ||
       com.startsWith(ANDOR_MAGIC_STRING);
   }
 
@@ -534,13 +535,13 @@ protected void initMetadataStore() throws FormatException {
     for (int i=0; i<getSizeC(); i++) {
       if (voltages != null && voltages[i] != null) {
         store.setDetectorSettingsVoltage(
-                new ElectricPotential(new Double(voltages[i]), UNITS.VOLT), 0, i);
+                new ElectricPotential(DataTools.parseDouble(voltages[i]), UNITS.VOLT), 0, i);
       }
       if (gains != null && gains[i] != null) {
-        store.setDetectorSettingsGain(new Double(gains[i]), 0, i);
+        store.setDetectorSettingsGain(DataTools.parseDouble(gains[i]), 0, i);
       }
       if (offsets != null && offsets[i] != null) {
-        store.setDetectorSettingsOffset(new Double(offsets[i]), 0, i);
+        store.setDetectorSettingsOffset(DataTools.parseDouble(offsets[i]), 0, i);
       }
       store.setDetectorType(MetadataTools.getDetectorType("Other"), 0, i);
       if (detectorManufacturer != null) {
@@ -572,13 +573,13 @@ protected void initMetadataStore() throws FormatException {
     }
 
     if (mag != null) {
-      store.setObjectiveCalibratedMagnification(new Double(mag), 0, 0);
+      store.setObjectiveCalibratedMagnification(DataTools.parseDouble(mag), 0, 0);
     }
 
     if (lensNA != null) {
       for (int i=0; i<getSizeC(); i++) {
         if (lensNA[i] != null) {
-          store.setObjectiveLensNA(new Double(lensNA[i]), 0, i);
+          store.setObjectiveLensNA(DataTools.parseDouble(lensNA[i]), 0, i);
         }
       }
     }
@@ -649,7 +650,7 @@ private void initAlternateMetadata() throws FormatException, IOException {
   private void initAlternateMetadataStore() throws FormatException {
     MetadataStore store = makeFilterMetadata();
     store.setImagingEnvironmentTemperature(
-      new Temperature(new Double(temperature.floatValue()), UNITS.CELSIUS), 0);
+      new Temperature(Double.valueOf(temperature.floatValue()), UNITS.CELSIUS), 0);
 
     String instrumentID = MetadataTools.createLSID("Instrument", 0);
     String detectorID = MetadataTools.createLSID("Detector", 0, 0);
@@ -661,14 +662,14 @@ private void initAlternateMetadataStore() throws FormatException {
 
     if (exposureTime != null) {
       for (int i=0; i<getImageCount(); i++) {
-        store.setPlaneExposureTime(new Time(new Double(exposureTime.floatValue()), UNITS.SECOND), 0, i);
+        store.setPlaneExposureTime(new Time(Double.valueOf(exposureTime.floatValue()), UNITS.SECOND), 0, i);
       }
     }
 
     for (int i=0; i<getEffectiveSizeC(); i++) {
       store.setDetectorSettingsID(detectorID, 0, i);
       store.setDetectorSettingsReadOutRate(
-        new Frequency(new Double(readoutTime.floatValue()), UNITS.HERTZ), 0, i);
+        new Frequency(Double.valueOf(readoutTime.floatValue()), UNITS.HERTZ), 0, i);
     }
   }
 
diff --git a/components/formats-gpl/src/loci/formats/in/GatanDM2Reader.java b/components/formats-gpl/src/loci/formats/in/GatanDM2Reader.java
index 477f001b6ed..569ba2b61b0 100644
--- a/components/formats-gpl/src/loci/formats/in/GatanDM2Reader.java
+++ b/components/formats-gpl/src/loci/formats/in/GatanDM2Reader.java
@@ -29,6 +29,7 @@
 
 import ome.xml.model.primitives.Timestamp;
 
+import loci.common.DataTools;
 import loci.common.DateTools;
 import loci.common.RandomAccessInputStream;
 import loci.formats.CoreMetadata;
@@ -382,11 +383,11 @@ else if (length == 1) {
           break;
         case 31:
           label = "Physical width";
-          pixelSizeX = new Double(value);
+          pixelSizeX = DataTools.parseDouble(value);
           break;
         case 32:
           label = "Physical height";
-          pixelSizeY = new Double(value);
+          pixelSizeY = DataTools.parseDouble(value);
           break;
         case 37:
           label = "Image label";
diff --git a/components/formats-gpl/src/loci/formats/in/GelReader.java b/components/formats-gpl/src/loci/formats/in/GelReader.java
index 1d0a2b36d41..6957d463302 100644
--- a/components/formats-gpl/src/loci/formats/in/GelReader.java
+++ b/components/formats-gpl/src/loci/formats/in/GelReader.java
@@ -204,7 +204,7 @@ else if (parsedTime != null) {
     }
 
     if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
-      Double pixelSize = new Double(scale.doubleValue());
+      Double pixelSize = Double.valueOf(scale.doubleValue());
       Length sizeX = FormatTools.getPhysicalSizeX(pixelSize);
       Length sizeY = FormatTools.getPhysicalSizeY(pixelSize);
       if (sizeX != null) {
diff --git a/components/formats-gpl/src/loci/formats/in/HRDGDFReader.java b/components/formats-gpl/src/loci/formats/in/HRDGDFReader.java
index c9e68351da7..a4b1894251a 100644
--- a/components/formats-gpl/src/loci/formats/in/HRDGDFReader.java
+++ b/components/formats-gpl/src/loci/formats/in/HRDGDFReader.java
@@ -129,14 +129,14 @@ protected void initFile(String id) throws FormatException, IOException {
     // size stored in kilometers
     String pixelSize =
       data[1].substring(data[1].indexOf(' ') + 1, data[1].lastIndexOf(" "));
-    Double physicalSize = new Double(pixelSize) * 1000000000.0;
+    Double physicalSize = DataTools.parseDouble(pixelSize) * 1000000000.0;
 
     // parse the center coordinates
     String centerLine = data[2];
     centerLine = centerLine.replaceAll("STORM CENTER LOCALE IS ", "");
     String[] center = centerLine.split(" ");
-    Double centerLongitude = new Double(center[0]);
-    Double centerLatitude = new Double(center[5]);
+    Double centerLongitude = DataTools.parseDouble(center[0]);
+    Double centerLatitude = DataTools.parseDouble(center[5]);
 
     // skip ahead to the surface wind section
 
@@ -161,9 +161,9 @@ protected void initFile(String id) throws FormatException, IOException {
 
         int comma = pixel.indexOf(',');
 
-        surfaceWind[0][pixIndex] = new Double(pixel.substring(0, comma).trim());
+        surfaceWind[0][pixIndex] = DataTools.parseDouble(pixel.substring(0, comma).trim());
         surfaceWind[1][pixIndex] =
-          new Double(pixel.substring(comma + 1).trim());
+          DataTools.parseDouble(pixel.substring(comma + 1).trim());
         pixIndex++;
       }
     }
diff --git a/components/formats-gpl/src/loci/formats/in/HamamatsuVMSReader.java b/components/formats-gpl/src/loci/formats/in/HamamatsuVMSReader.java
index d54ecbeeba7..46ef5b33688 100644
--- a/components/formats-gpl/src/loci/formats/in/HamamatsuVMSReader.java
+++ b/components/formats-gpl/src/loci/formats/in/HamamatsuVMSReader.java
@@ -32,6 +32,7 @@
 import java.util.HashMap;
 
 import loci.common.Constants;
+import loci.common.DataTools;
 import loci.common.IniList;
 import loci.common.IniParser;
 import loci.common.IniTable;
@@ -258,12 +259,12 @@ protected void initFile(String id) throws FormatException, IOException {
     String optimisationFile = slideInfo.get("OptimisationFile");
     macroFile = slideInfo.get("MacroImage");
 
-    Double physicalWidth = new Double(slideInfo.get("PhysicalWidth"));
-    Double physicalHeight = new Double(slideInfo.get("PhysicalHeight"));
-    Double magnification = new Double(slideInfo.get("SourceLens"));
+    Double physicalWidth = DataTools.parseDouble(slideInfo.get("PhysicalWidth"));
+    Double physicalHeight = DataTools.parseDouble(slideInfo.get("PhysicalHeight"));
+    Double magnification = DataTools.parseDouble(slideInfo.get("SourceLens"));
 
-    Double macroWidth = new Double(slideInfo.get("PhysicalMacroWidth"));
-    Double macroHeight = new Double(slideInfo.get("PhysicalMacroHeight"));
+    Double macroWidth = DataTools.parseDouble(slideInfo.get("PhysicalMacroWidth"));
+    Double macroHeight = DataTools.parseDouble(slideInfo.get("PhysicalMacroHeight"));
 
     for (String key : slideInfo.keySet()) {
       if (!IniTable.HEADER_KEY.equals(key)) {
diff --git a/components/formats-gpl/src/loci/formats/in/HitachiReader.java b/components/formats-gpl/src/loci/formats/in/HitachiReader.java
index 4bd20564ca8..5b57b396396 100644
--- a/components/formats-gpl/src/loci/formats/in/HitachiReader.java
+++ b/components/formats-gpl/src/loci/formats/in/HitachiReader.java
@@ -304,7 +304,7 @@ private void populateOMEMetadata(IniTable image, MetadataStore store) {
 
     String modelNumber = image.get("InstructName");
     String serialNumber = image.get("SerialNumber");
-    Double pixelSize = new Double(image.get("PixelSize"));
+    Double pixelSize = DataTools.parseDouble(image.get("PixelSize"));
 
     String workingDistance = image.get("WorkingDistance");
 
@@ -349,7 +349,7 @@ private void populateOMEMetadata(IniTable image, MetadataStore store) {
       String objective = MetadataTools.createLSID("Objective", 0, 0);
       store.setObjectiveID(objective, 0, 0);
       store.setObjectiveSettingsID(objective, 0);
-      store.setObjectiveWorkingDistance(new Length(new Double(workingDistance), UNITS.MICROMETER), 0, 0);
+      store.setObjectiveWorkingDistance(new Length(DataTools.parseDouble(workingDistance), UNITS.MICROMETER), 0, 0);
     }
   }
 }
diff --git a/components/formats-gpl/src/loci/formats/in/IMODReader.java b/components/formats-gpl/src/loci/formats/in/IMODReader.java
index 8cc5a864ac6..1abd07d4870 100644
--- a/components/formats-gpl/src/loci/formats/in/IMODReader.java
+++ b/components/formats-gpl/src/loci/formats/in/IMODReader.java
@@ -28,6 +28,7 @@
 import java.io.IOException;
 import java.util.ArrayList;
 
+import loci.common.DataTools;
 import loci.common.RandomAccessInputStream;
 import loci.formats.CoreMetadata;
 import loci.formats.FormatException;
@@ -307,16 +308,16 @@ protected void initFile(String id) throws FormatException, IOException {
               store.setPointID(shapeID, obj, nextShape);
               store.setPointStrokeColor(
                 new Color(r, g, b, 0xff), obj, nextShape);
-              l = new Length(new Double(lineWidth2D), UNITS.PIXEL);
+              l = new Length(Double.valueOf(lineWidth2D), UNITS.PIXEL);
               store.setPointStrokeWidth(l, obj, nextShape);
               if (lineStyle == 1) {
                 store.setPointStrokeDashArray("5", obj, nextShape);
               }
 
               store.setPointX(
-                new Double(points[obj][contour][i][0]), obj, nextShape);
+                Double.valueOf(points[obj][contour][i][0]), obj, nextShape);
               store.setPointY(
-                new Double(points[obj][contour][i][1]), obj, nextShape);
+                Double.valueOf(points[obj][contour][i][1]), obj, nextShape);
               if (points[obj][contour][i][2] >= 0) {
                 store.setPointTheZ(new NonNegativeInteger(
                   (int) points[obj][contour][i][2]), obj, nextShape);
@@ -347,7 +348,7 @@ protected void initFile(String id) throws FormatException, IOException {
               store.setPolygonID(shapeID, obj, nextShape);
               store.setPolygonStrokeColor(
                 new Color(r, g, b, 0xff), obj, nextShape);
-              l = new Length(new Double(lineWidth2D), UNITS.PIXEL);
+              l = new Length(Double.valueOf(lineWidth2D), UNITS.PIXEL);
               store.setPolygonStrokeWidth(l, obj, nextShape);
               if (lineStyle == 1) {
                 store.setPolygonStrokeDashArray("5", obj, nextShape);
@@ -363,7 +364,7 @@ protected void initFile(String id) throws FormatException, IOException {
               store.setPolylineID(shapeID, obj, nextShape);
               store.setPolylineStrokeColor(
                 new Color(r, g, b, 0xff), obj, nextShape);
-              l = new Length(new Double(lineWidth2D), UNITS.PIXEL);
+              l = new Length(Double.valueOf(lineWidth2D), UNITS.PIXEL);
               store.setPolylineStrokeWidth(l, obj, nextShape);
               if (lineStyle == 1) {
                 store.setPolylineStrokeDashArray("5", obj, nextShape);
diff --git a/components/formats-gpl/src/loci/formats/in/INRReader.java b/components/formats-gpl/src/loci/formats/in/INRReader.java
index f04b8ef4923..459145c6278 100644
--- a/components/formats-gpl/src/loci/formats/in/INRReader.java
+++ b/components/formats-gpl/src/loci/formats/in/INRReader.java
@@ -27,6 +27,7 @@
 
 import java.io.IOException;
 
+import loci.common.DataTools;
 import loci.common.RandomAccessInputStream;
 import loci.formats.CoreMetadata;
 import loci.formats.FormatException;
@@ -131,13 +132,13 @@ else if (key.equals("PIXSIZE")) {
           nBits = Integer.parseInt(bits);
         }
         else if (key.equals("VX")) {
-          physicalSizeX = new Double(value);
+          physicalSizeX = DataTools.parseDouble(value);
         }
         else if (key.equals("VY")) {
-          physicalSizeY = new Double(value);
+          physicalSizeY = DataTools.parseDouble(value);
         }
         else if (key.equals("VZ")) {
-          physicalSizeZ = new Double(value);
+          physicalSizeZ = DataTools.parseDouble(value);
         }
       }
     }
diff --git a/components/formats-gpl/src/loci/formats/in/IPLabReader.java b/components/formats-gpl/src/loci/formats/in/IPLabReader.java
index 922e1bade09..3c0a740f715 100644
--- a/components/formats-gpl/src/loci/formats/in/IPLabReader.java
+++ b/components/formats-gpl/src/loci/formats/in/IPLabReader.java
@@ -302,10 +302,10 @@ else if (tag.equals("roi ") &&
         int numRoiPts = in.readInt();
 
         store.setRectangleID(MetadataTools.createLSID("Shape", 0, 0), 0, 0);
-        store.setRectangleX(new Double(roiLeft), 0, 0);
-        store.setRectangleY(new Double(roiTop), 0, 0);
-        store.setRectangleWidth(new Double(roiRight - roiLeft), 0, 0);
-        store.setRectangleHeight(new Double(roiBottom - roiTop), 0, 0);
+        store.setRectangleX(Double.valueOf(roiLeft), 0, 0);
+        store.setRectangleY(Double.valueOf(roiTop), 0, 0);
+        store.setRectangleWidth(Double.valueOf(roiRight - roiLeft), 0, 0);
+        store.setRectangleHeight(Double.valueOf(roiBottom - roiTop), 0, 0);
         String roiID = MetadataTools.createLSID("ROI", 0, 0);
         store.setROIID(roiID, 0);
         store.setImageROIRef(roiID, 0, 0);
@@ -345,7 +345,7 @@ else if (tag.equals("unit")) {
               break;
           }
 
-          if (i == 0) pixelSize = new Double(unitsPerPixel);
+          if (i == 0) pixelSize = Double.valueOf(unitsPerPixel);
 
           addGlobalMetaList("UnitName", xUnitName);
         }
@@ -396,11 +396,11 @@ else if (tagBytes[0] == 0x1a && tagBytes[1] == (byte) 0xd9 &&
           for (int c=0; c<getSizeC(); c++) {
             for (int z=0; z<getSizeZ(); z++) {
               int plane = getIndex(z, c, i);
-              store.setPlaneDeltaT(new Time(new Double(timepoint), UNITS.SECOND), 0, plane);
+              store.setPlaneDeltaT(new Time(Double.valueOf(timepoint), UNITS.SECOND), 0, plane);
             }
           }
           if (i == 1) {
-            timeIncrement = new Double(timepoint);
+            timeIncrement = Double.valueOf(timepoint);
           }
         }
       }
diff --git a/components/formats-gpl/src/loci/formats/in/IPWReader.java b/components/formats-gpl/src/loci/formats/in/IPWReader.java
index d06d3f16a42..1804f0eac4c 100644
--- a/components/formats-gpl/src/loci/formats/in/IPWReader.java
+++ b/components/formats-gpl/src/loci/formats/in/IPWReader.java
@@ -274,7 +274,7 @@ else if (relativePath.equals("ImageTIFF")) {
           idx = name.substring(21, name.indexOf(File.separator, 22));
         }
 
-        imageFiles.put(new Integer(idx), name);
+        imageFiles.put(Integer.parseInt(idx), name);
       }
     }
 
diff --git a/components/formats-gpl/src/loci/formats/in/ImarisHDFReader.java b/components/formats-gpl/src/loci/formats/in/ImarisHDFReader.java
index 96ce60737f9..ba4de1d39d3 100644
--- a/components/formats-gpl/src/loci/formats/in/ImarisHDFReader.java
+++ b/components/formats-gpl/src/loci/formats/in/ImarisHDFReader.java
@@ -370,25 +370,25 @@ protected void initFile(String id) throws FormatException, IOException {
 
         if (cIndex < gain.size()) {
           try {
-            gainValue = new Float(gain.get(cIndex));
+            gainValue = Float.parseFloat(gain.get(cIndex));
           }
           catch (NumberFormatException e) { }
         }
         if (cIndex < pinhole.size()) {
           try {
-            pinholeValue = new Integer(pinhole.get(cIndex));
+            pinholeValue = Integer.parseInt(pinhole.get(cIndex));
           }
           catch (NumberFormatException e) { }
         }
         if (cIndex < emWave.size()) {
           try {
-            emWaveValue = new Integer(emWave.get(cIndex));
+            emWaveValue = Integer.parseInt(emWave.get(cIndex));
           }
           catch (NumberFormatException e) { }
         }
         if (cIndex < exWave.size()) {
           try {
-            exWaveValue = new Integer(exWave.get(cIndex));
+            exWaveValue = Integer.parseInt(exWave.get(cIndex));
           }
           catch (NumberFormatException e) { }
         }
@@ -397,13 +397,13 @@ protected void initFile(String id) throws FormatException, IOException {
 
         if (cIndex < channelMin.size()) {
           try {
-            minValue = new Double(channelMin.get(cIndex));
+            minValue = DataTools.parseDouble(channelMin.get(cIndex));
           }
           catch (NumberFormatException e) { }
         }
         if (cIndex < channelMax.size()) {
           try {
-            maxValue = new Double(channelMax.get(cIndex));
+            maxValue = DataTools.parseDouble(channelMax.get(cIndex));
           }
           catch (NumberFormatException e) { }
         }
diff --git a/components/formats-gpl/src/loci/formats/in/ImarisTiffReader.java b/components/formats-gpl/src/loci/formats/in/ImarisTiffReader.java
index ddb6bc5d2fc..8f2e77905b8 100644
--- a/components/formats-gpl/src/loci/formats/in/ImarisTiffReader.java
+++ b/components/formats-gpl/src/loci/formats/in/ImarisTiffReader.java
@@ -33,6 +33,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import loci.common.DataTools;
 import loci.formats.CoreMetadata;
 import loci.formats.FormatException;
 import loci.formats.FormatTools;
@@ -145,11 +146,11 @@ protected void initFile(String id) throws FormatException, IOException {
             description = value;
           }
           else if (key.equals("LSMEmissionWavelength") && !value.equals("0")) {
-            emWave.add(new Double(value));
+            emWave.add(DataTools.parseDouble(value));
           }
           else if (key.equals("LSMExcitationWavelength") && !value.equals("0"))
           {
-            exWave.add(new Double(value));
+            exWave.add(DataTools.parseDouble(value));
           }
           else if (key.equals("Name") && !currentId.endsWith(value)) {
             channelNames.add(value);
diff --git a/components/formats-gpl/src/loci/formats/in/InCellReader.java b/components/formats-gpl/src/loci/formats/in/InCellReader.java
index 53e343f1693..2c8cdd988ac 100644
--- a/components/formats-gpl/src/loci/formats/in/InCellReader.java
+++ b/components/formats-gpl/src/loci/formats/in/InCellReader.java
@@ -1047,7 +1047,7 @@ else if (qName.equals("ObjectiveCalibration")) {
         Double mag =
           Double.parseDouble(attributes.getValue("magnification"));
         store.setObjectiveNominalMagnification(mag, 0, 0);
-        store.setObjectiveLensNA(new Double(
+        store.setObjectiveLensNA(DataTools.parseDouble(
           attributes.getValue("numerical_aperture")), 0, 0);
         try {
          store.setObjectiveImmersion(MetadataTools.getImmersion("Other"), 0, 0);
@@ -1068,20 +1068,20 @@ else if (qName.equals("ObjectiveCalibration")) {
           LOGGER.warn("", e);
         }
 
-        Double pixelSizeX = new Double(attributes.getValue("pixel_width"));
-        Double pixelSizeY = new Double(attributes.getValue("pixel_height"));
-        refractive = new Double(attributes.getValue("refractive_index"));
+        Double pixelSizeX = DataTools.parseDouble(attributes.getValue("pixel_width"));
+        Double pixelSizeY = DataTools.parseDouble(attributes.getValue("pixel_height"));
+        refractive = DataTools.parseDouble(attributes.getValue("refractive_index"));
 
         x = FormatTools.getPhysicalSizeX(pixelSizeX);
         y = FormatTools.getPhysicalSizeY(pixelSizeY);
       }
       else if (qName.equals("ExcitationFilter")) {
         String wave = attributes.getValue("wavelength");
-        if (wave != null) exWaves.add(new Double(wave));
+        if (wave != null) exWaves.add(DataTools.parseDouble(wave));
       }
       else if (qName.equals("EmissionFilter")) {
         String wave = attributes.getValue("wavelength");
-        if (wave != null) emWaves.add(new Double(wave));
+        if (wave != null) emWaves.add(DataTools.parseDouble(wave));
         channelNames.add(attributes.getValue("name"));
       }
       else if (qName.equals("Camera")) {
@@ -1106,14 +1106,14 @@ else if (qName.equals("Gain")) {
           return;
         }
         try {
-          gain = new Double(value);
+          gain = DataTools.parseDouble(value);
         }
         catch (NumberFormatException e) {
           LOGGER.debug("Could not parse gain '" + value + "'", e);
         }
       }
       else if (qName.equals("PlateTemperature")) {
-        temperature = new Double(attributes.getValue("value"));
+        temperature = DataTools.parseDouble(attributes.getValue("value"));
       }
       else if (qName.equals("Plate")) {
         nextPlate++;
diff --git a/components/formats-gpl/src/loci/formats/in/InveonReader.java b/components/formats-gpl/src/loci/formats/in/InveonReader.java
index d271876c92c..457cc1896e9 100644
--- a/components/formats-gpl/src/loci/formats/in/InveonReader.java
+++ b/components/formats-gpl/src/loci/formats/in/InveonReader.java
@@ -335,13 +335,22 @@ else if (key.equals("data_file_pointer")) {
         }
         // pixel sizes stored in mm
         else if (key.equals("pixel_size_x")) {
-          pixelSizeX = new Double(value) * 1000;
+          Double size = DataTools.parseDouble(value);
+          if (size != null) {
+            pixelSizeX = size * 1000;
+          }
         }
         else if (key.equals("pixel_size_y")) {
-          pixelSizeY = new Double(value) * 1000;
+          Double size = DataTools.parseDouble(value);
+          if (size != null) {
+            pixelSizeY = size * 1000;
+          }
         }
         else if (key.equals("pixel_size_z")) {
-          pixelSizeZ = new Double(value) * 1000;
+          Double size = DataTools.parseDouble(value);
+          if (size != null) {
+            pixelSizeZ = size * 1000;
+          }
         }
 
         addGlobalMeta(key, value);
diff --git a/components/formats-gpl/src/loci/formats/in/IvisionReader.java b/components/formats-gpl/src/loci/formats/in/IvisionReader.java
index 22b758de9b5..23efc4766e4 100644
--- a/components/formats-gpl/src/loci/formats/in/IvisionReader.java
+++ b/components/formats-gpl/src/loci/formats/in/IvisionReader.java
@@ -27,6 +27,7 @@
 
 import java.io.IOException;
 
+import loci.common.DataTools;
 import loci.common.DateTools;
 import loci.common.RandomAccessInputStream;
 import loci.common.xml.BaseHandler;
@@ -293,7 +294,7 @@ protected void initFile(String id) throws FormatException, IOException {
       if (deltaT != null) {
         Double increment = 0d;
         try {
-          increment = new Double(deltaT);
+          increment = DataTools.parseDouble(deltaT);
         }
         catch (NumberFormatException e) {
           LOGGER.debug("Failed to parse time increment", e);
@@ -327,7 +328,7 @@ protected void initFile(String id) throws FormatException, IOException {
       store.setDetectorSettingsBinning(MetadataTools.getBinning(binX + "x" + binY), 0, 0);
       if (gain != null) {
         try {
-          store.setDetectorSettingsGain(new Double(gain), 0, 0);
+          store.setDetectorSettingsGain(DataTools.parseDouble(gain), 0, 0);
         }
         catch (NumberFormatException e) {
           LOGGER.debug("Failed to parse detector gain", e);
@@ -359,19 +360,19 @@ public void endElement(String uri, String localName, String qName) {
       else if ("iplab:Interval_T".equals(key)) deltaT = value;
       else if ("iplab:Objective_Mag".equals(key)) {
         try {
-          magnification = new Double(value);
+          magnification = DataTools.parseDouble(value);
         }
         catch (NumberFormatException e) { }
       }
       else if ("iplab:Objective_NA".equals(key)) {
         try {
-          lensNA = new Double(value);
+          lensNA = DataTools.parseDouble(value);
         }
         catch (NumberFormatException e) { }
       }
       else if ("iplab:Objective_RI".equals(key)) {
         try {
-          refractiveIndex = new Double(value);
+          refractiveIndex = DataTools.parseDouble(value);
         }
         catch (NumberFormatException e) { }
       }
diff --git a/components/formats-gpl/src/loci/formats/in/KodakReader.java b/components/formats-gpl/src/loci/formats/in/KodakReader.java
index 2dd72f6be94..77cc26ea569 100644
--- a/components/formats-gpl/src/loci/formats/in/KodakReader.java
+++ b/components/formats-gpl/src/loci/formats/in/KodakReader.java
@@ -30,6 +30,7 @@
 import java.util.regex.Pattern;
 
 import loci.common.Constants;
+import loci.common.DataTools;
 import loci.common.DateTools;
 import loci.common.RandomAccessInputStream;
 import loci.formats.CoreMetadata;
@@ -204,7 +205,7 @@ else if (key.equals("Capture Time/Date")) {
         }
       }
       else if (key.equals("Exposure Time")) {
-        Double exposureTime = new Double(value.substring(0, value.indexOf(' ')));
+        Double exposureTime = DataTools.parseDouble(value.substring(0, value.indexOf(' ')));
         if (exposureTime != null) {
           store.setPlaneExposureTime(new Time(exposureTime, UNITS.SECOND), 0, 0);
         }
@@ -214,7 +215,7 @@ else if (key.equals("Vertical Resolution")) {
         if (value.indexOf(' ') > 0) {
           value = value.substring(0, value.indexOf(' '));
         }
-        Double size = new Double(value);
+        Double size = DataTools.parseDouble(value);
         size = 1.0 / (size * (1.0 / 25400));
 
         Length sizeY = FormatTools.getPhysicalSizeY(size);
@@ -227,7 +228,7 @@ else if (key.equals("Horizontal Resolution")) {
         if (value.indexOf(' ') > 0) {
           value = value.substring(0, value.indexOf(' '));
         }
-        Double size = new Double(value);
+        Double size = DataTools.parseDouble(value);
         size = 1.0 / (size * (1.0 / 25400));
 
         Length sizeX = FormatTools.getPhysicalSizeX(size);
@@ -240,11 +241,11 @@ else if (key.equals("CCD Temperature")) {
         Matcher hexMatcher = Pattern.compile("0x([0-9A-F]+)").matcher(value);
         if (hexMatcher.matches()) {
           // CCD temperature stored as a hexadecimal string such as "0xEB".
-          temp = new Double(Integer.parseInt(hexMatcher.group(1), 16));
+          temp = Double.valueOf(Integer.parseInt(hexMatcher.group(1), 16));
           LOGGER.debug("CCD temperature detected as {}; assumed to be invalid", temp);
         }
         else {
-          temp = new Double(value.substring(0, value.indexOf(' ')));
+          temp = DataTools.parseDouble(value.substring(0, value.indexOf(' ')));
           store.setImagingEnvironmentTemperature(
                 new Temperature(temp, UNITS.CELSIUS), 0);
         }
diff --git a/components/formats-gpl/src/loci/formats/in/L2DReader.java b/components/formats-gpl/src/loci/formats/in/L2DReader.java
index a55515d06bf..3f3efd4a379 100644
--- a/components/formats-gpl/src/loci/formats/in/L2DReader.java
+++ b/components/formats-gpl/src/loci/formats/in/L2DReader.java
@@ -353,7 +353,7 @@ else if (key.equals("ScanChannels")) {
           for (int q=0; q<waves.length; q++) {
             String laser = MetadataTools.createLSID("LightSource", 0, q);
             store.setLaserID(laser, 0, q);
-            Double wave = new Double(waves[q].trim());
+            Double wave = DataTools.parseDouble(waves[q].trim());
             Length wavelength = FormatTools.getWavelength(wave);
             if (wavelength != null) {
               store.setLaserWavelength(wavelength, 0, q);
diff --git a/components/formats-gpl/src/loci/formats/in/LIFReader.java b/components/formats-gpl/src/loci/formats/in/LIFReader.java
index 33e342ee3a8..9ea3f61c73c 100644
--- a/components/formats-gpl/src/loci/formats/in/LIFReader.java
+++ b/components/formats-gpl/src/loci/formats/in/LIFReader.java
@@ -1830,7 +1830,7 @@ else if (objectClass.equals("CDetectionUnit")) {
           int channel = getChannelIndex(filterSetting);
           if (channel < 0) continue;
 
-          detectorIndexes[image].put(new Integer(data), object);
+          detectorIndexes[image].put(Integer.parseInt(data), object);
           activeDetector[image].add("Active".equals(variant.trim()));
         }
       }
diff --git a/components/formats-gpl/src/loci/formats/in/LeicaHandler.java b/components/formats-gpl/src/loci/formats/in/LeicaHandler.java
index bcc54a85c86..e5d4fdbbca0 100644
--- a/components/formats-gpl/src/loci/formats/in/LeicaHandler.java
+++ b/components/formats-gpl/src/loci/formats/in/LeicaHandler.java
@@ -37,6 +37,7 @@
 import java.util.StringTokenizer;
 import java.util.Vector;
 
+import loci.common.DataTools;
 import loci.common.DateTools;
 import loci.common.xml.BaseHandler;
 import loci.formats.CoreMetadata;
@@ -397,7 +398,7 @@ else if (qName.equals("ChannelDescription")) {
       String bytesInc = attributes.getValue("BytesInc");
       int bytes = bytesInc == null ? 0 : Integer.parseInt(bytesInc);
       if (bytes > 0) {
-        bytesPerAxis.put(new Integer(bytes), "C");
+        bytesPerAxis.put(Integer.valueOf(bytes), "C");
       }
     }
     else if (qName.equals("DimensionDescription")) {
@@ -415,7 +416,7 @@ else if (unit.equals("m")) {
         physicalLen *= 1000000;
       }
 
-      Double physicalSize = new Double(physicalLen);
+      Double physicalSize = Double.valueOf(physicalLen);
 
       CoreMetadata coreMeta = core.get(core.size() - 1);
 
@@ -445,11 +446,11 @@ else if (unit.equals("m")) {
           if (coreMeta.sizeY != 0) {
             if (coreMeta.sizeZ == 1) {
               coreMeta.sizeZ = len;
-              bytesPerAxis.put(new Integer(nBytes), "Z");
+              bytesPerAxis.put(Integer.valueOf(nBytes), "Z");
             }
             else if (coreMeta.sizeT == 1) {
               coreMeta.sizeT = len;
-              bytesPerAxis.put(new Integer(nBytes), "T");
+              bytesPerAxis.put(Integer.valueOf(nBytes), "T");
             }
           }
           else {
@@ -471,11 +472,11 @@ else if (coreMeta.sizeT == 1) {
             if (sizeY != null) {
               store.setPixelsPhysicalSizeY(sizeY, numDatasets);
             }
-            bytesPerAxis.put(new Integer(nBytes), "Y");
+            bytesPerAxis.put(Integer.valueOf(nBytes), "Y");
           }
           else {
             coreMeta.sizeZ = len;
-            bytesPerAxis.put(new Integer(nBytes), "Z");
+            bytesPerAxis.put(Integer.valueOf(nBytes), "Z");
           }
           break;
         case 4: // T axis
@@ -488,11 +489,11 @@ else if (coreMeta.sizeT == 1) {
             if (sizeY != null) {
               store.setPixelsPhysicalSizeY(sizeY, numDatasets);
             }
-            bytesPerAxis.put(new Integer(nBytes), "Y");
+            bytesPerAxis.put(Integer.valueOf(nBytes), "Y");
           }
           else {
             coreMeta.sizeT = len;
-            bytesPerAxis.put(new Integer(nBytes), "T");
+            bytesPerAxis.put(Integer.valueOf(nBytes), "T");
           }
           break;
         default:
@@ -511,10 +512,10 @@ else if (qName.equals("ScannerSettingRecord") &&
         store.setMicroscopeType(MicroscopeType.OTHER, numDatasets);
       }
       else if (id.equals("dblPinhole")) {
-        pinhole = new Double(Double.parseDouble(value) * 1000000);
+        pinhole = Double.valueOf(Double.parseDouble(value) * 1000000);
       }
       else if (id.equals("dblZoom")) {
-        zoom = new Double(value);
+        zoom = DataTools.parseDouble(value);
       }
       else if (id.equals("dblStepSize")) {
         double zStep = Double.parseDouble(value) * 1000000;
@@ -524,7 +525,7 @@ else if (id.equals("dblStepSize")) {
         }
       }
       else if (id.equals("nDelayTime_s")) {
-        Double timeIncrement = new Double(value);
+        Double timeIncrement = DataTools.parseDouble(value);
         if (timeIncrement != null) {
           store.setPixelsTimeIncrement(new Time(timeIncrement, UNITS.SECOND), numDatasets);
         }
@@ -542,7 +543,7 @@ else if (id.indexOf("WFC") == 1) {
         if (channel == null) channel = new Channel();
         if (id.endsWith("ExposureTime") && c < numChannels) {
           try {
-            Double exposureTime = new Double(value);
+            Double exposureTime = DataTools.parseDouble(value);
             if (exposureTime != null) {
               store.setPlaneExposureTime(new Time(exposureTime, UNITS.SECOND), numDatasets, c);
             }
@@ -550,7 +551,7 @@ else if (id.indexOf("WFC") == 1) {
           catch (IndexOutOfBoundsException e) { }
         }
         else if (id.endsWith("Gain")) {
-          channel.gain = new Double(value);
+          channel.gain = DataTools.parseDouble(value);
 
           String detectorID =
             MetadataTools.createLSID("Detector", numDatasets, 0);
@@ -559,7 +560,7 @@ else if (id.endsWith("Gain")) {
           store.setDetectorType(DetectorType.CCD, numDatasets, 0);
         }
         else if (id.endsWith("WaveLength")) {
-          Double exWave = new Double(value);
+          Double exWave = DataTools.parseDouble(value);
           Length ex = FormatTools.getExcitationWavelength(exWave);
           if (ex != null) {
             channel.exWave = ex;
@@ -582,7 +583,7 @@ else if (qName.equals("FilterSettingRecord") &&
       CoreMetadata coreMeta = core.get(numDatasets);
 
       if (attribute.equals("NumericalAperture")) {
-        store.setObjectiveLensNA(new Double(variant), numDatasets, 0);
+        store.setObjectiveLensNA(DataTools.parseDouble(variant), numDatasets, 0);
       }
       else if (attribute.equals("OrderNumber")) {
         store.setObjectiveSerialNumber(variant, numDatasets, 0);
@@ -601,11 +602,11 @@ else if (objectClass.equals("CDetectionUnit")) {
         }
         else if (attribute.equals("HighVoltage")) {
           Detector d = detectors.get(detectors.size() - 1);
-          d.voltage = new Double(variant);
+          d.voltage = DataTools.parseDouble(variant);
         }
         else if (attribute.equals("VideoOffset")) {
           Detector d = detectors.get(detectors.size() - 1);
-          d.offset = new Double(variant);
+          d.offset = DataTools.parseDouble(variant);
         }
       }
       else if (attribute.equals("Objective")) {
@@ -622,7 +623,7 @@ else if (attribute.equals("Objective")) {
             String na = token.substring(x + 1);
 
             store.setObjectiveNominalMagnification(mag, numDatasets, 0);
-            store.setObjectiveLensNA(new Double(na), numDatasets, 0);
+            store.setObjectiveLensNA(DataTools.parseDouble(na), numDatasets, 0);
           }
           else {
             model.append(token);
@@ -664,7 +665,7 @@ else if (attribute.equals("RefractionIndex")) {
         String id = MetadataTools.createLSID("Objective", numDatasets, 0);
         store.setObjectiveID(id, numDatasets, 0);
         store.setObjectiveSettingsID(id, numDatasets);
-        store.setObjectiveSettingsRefractiveIndex(new Double(variant),
+        store.setObjectiveSettingsRefractiveIndex(DataTools.parseDouble(variant),
           numDatasets);
       }
       else if (attribute.equals("XPos")) {
@@ -725,9 +726,9 @@ else if (attributes.getValue("Description").endsWith("(right)")) {
     }
     else if (qName.equals("Detector") && level != MetadataLevel.MINIMUM) {
       String v = attributes.getValue("Gain");
-      Double gain = v == null ? null : new Double(v);
+      Double gain = v == null ? null : DataTools.parseDouble(v);
       v = attributes.getValue("Offset");
-      Double offset = v == null ? null : new Double(v);
+      Double offset = v == null ? null : DataTools.parseDouble(v);
       boolean active = "1".equals(attributes.getValue("IsActive"));
 
       if (active) {
@@ -832,7 +833,7 @@ else if (qName.equals("LaserLineSetting") && level != MetadataLevel.MINIMUM)
       l.index += (2 - (qualifier / 10));
       if (l.index < 0) l.index = 0;
       l.id = MetadataTools.createLSID("LightSource", numDatasets, l.index);
-      l.wavelength = new Double(attributes.getValue("LaserLine"));
+      l.wavelength = DataTools.parseDouble(attributes.getValue("LaserLine"));
       while (l.index > laserCount) {
         String lsid =
           MetadataTools.createLSID("LightSource", numDatasets, laserCount);
@@ -890,7 +891,7 @@ else if (qName.equals("RelTimeStamp") && level != MetadataLevel.MINIMUM) {
       CoreMetadata coreMeta = core.get(numDatasets);
       int nImages = coreMeta.sizeZ * coreMeta.sizeT * coreMeta.sizeC;
       if (count < nImages) {
-        Double time = new Double(attributes.getValue("Time"));
+        Double time = DataTools.parseDouble(attributes.getValue("Time"));
         if (time != null) {
           store.setPlaneDeltaT(new Time(time, UNITS.SECOND), numDatasets, count++);
         }
@@ -919,11 +920,11 @@ else if (qName.equals("Vertex") && level != MetadataLevel.MINIMUM) {
       String y = attributes.getValue("y");
       if (x != null) {
         x = x.replaceAll(",", ".");
-        roi.x.add(new Double(x));
+        roi.x.add(DataTools.parseDouble(x));
       }
       if (y != null) {
         y = y.replaceAll(",", ".");
-        roi.y.add(new Double(y));
+        roi.y.add(DataTools.parseDouble(y));
       }
     }
     else if (qName.equals("ROI")) {
@@ -1038,7 +1039,7 @@ public void storeROI(MetadataStore store, int series, int roi) {
           store.setLabelFontSize(fontSize, roi, 0);
         }
       }
-      Length l = new Length(new Double(linewidth), UNITS.PIXEL);
+      Length l = new Length(Double.valueOf(linewidth), UNITS.PIXEL);
       store.setLabelStrokeWidth(l, roi, 0);
 
       if (!normalized) normalize();
diff --git a/components/formats-gpl/src/loci/formats/in/LeicaReader.java b/components/formats-gpl/src/loci/formats/in/LeicaReader.java
index 2ec4d813d53..5f890fb32f5 100644
--- a/components/formats-gpl/src/loci/formats/in/LeicaReader.java
+++ b/components/formats-gpl/src/loci/formats/in/LeicaReader.java
@@ -211,7 +211,7 @@ public boolean isThisType(RandomAccessInputStream stream) throws IOException {
     TiffParser tp = new TiffParser(stream);
     IFD ifd = tp.getFirstIFD();
     if (ifd == null) return false;
-    return ifd.containsKey(new Integer(LEICA_MAGIC_TAG));
+    return ifd.containsKey(Integer.valueOf(LEICA_MAGIC_TAG));
   }
 
   /* @see loci.formats.IFormatReader#get8BitLookupTable() */
@@ -1339,10 +1339,10 @@ private void parseInstrumentData(MetadataStore store, int blockNum)
 
           try {
             if (tokens[2].equals("VideoOffset")) {
-              detector.offset = new Double(data);
+              detector.offset = DataTools.parseDouble(data);
             }
             else if (tokens[2].equals("HighVoltage")) {
-              detector.voltage = new Double(data);
+              detector.voltage = DataTools.parseDouble(data);
             }
             else if (tokens[2].equals("State")) {
               detector.active = data.equals("Active");
@@ -1369,7 +1369,7 @@ else if (tokens[0].startsWith("CTurret")) {
 
         int objective = Integer.parseInt(tokens[3]);
         if (tokens[2].equals("NumericalAperture")) {
-          store.setObjectiveLensNA(new Double(data), series, objective);
+          store.setObjectiveLensNA(DataTools.parseDouble(data), series, objective);
         }
         else if (tokens[2].equals("Objective")) {
           String[] objectiveData = data.split(" ");
@@ -1420,7 +1420,7 @@ else if (immersion == null) {
           store.setObjectiveCorrection(
             MetadataTools.getCorrection(correction), series, objective);
           store.setObjectiveModel(model.toString().trim(), series, objective);
-          store.setObjectiveLensNA(new Double(na), series, objective);
+          store.setObjectiveLensNA(DataTools.parseDouble(na), series, objective);
 
           Double magnification = Double.parseDouble(mag);
           store.setObjectiveNominalMagnification(
@@ -1430,7 +1430,7 @@ else if (tokens[2].equals("OrderNumber")) {
           store.setObjectiveSerialNumber(data, series, objective);
         }
         else if (tokens[2].equals("RefractionIndex")) {
-          store.setObjectiveSettingsRefractiveIndex(new Double(data), series);
+          store.setObjectiveSettingsRefractiveIndex(DataTools.parseDouble(data), series);
         }
 
         // link Objective to Image
@@ -1609,14 +1609,14 @@ else if (contentID.startsWith("nDelayTime")) {
           }
         }
         if (channel < emWaves[i].size()) {
-          Double wave = new Double(emWaves[i].get(channel).toString());
+          Double wave = DataTools.parseDouble(emWaves[i].get(channel).toString());
           Length emission = FormatTools.getEmissionWavelength(wave);
           if (emission != null) {
             store.setChannelEmissionWavelength(emission, i, channel);
           }
         }
         if (channel < exWaves[i].size()) {
-          Double wave = new Double(exWaves[i].get(channel).toString());
+          Double wave = DataTools.parseDouble(exWaves[i].get(channel).toString());
           Length ex = FormatTools.getExcitationWavelength(wave);
           if (ex != null) {
             store.setChannelExcitationWavelength(ex, i, channel);
diff --git a/components/formats-gpl/src/loci/formats/in/LeicaSCNReader.java b/components/formats-gpl/src/loci/formats/in/LeicaSCNReader.java
index f6e76d32afc..276cedf8c27 100644
--- a/components/formats-gpl/src/loci/formats/in/LeicaSCNReader.java
+++ b/components/formats-gpl/src/loci/formats/in/LeicaSCNReader.java
@@ -45,6 +45,7 @@
 import ome.xml.model.enums.IlluminationType;
 import ome.xml.model.primitives.Timestamp;
 
+import loci.common.DataTools;
 import loci.common.RandomAccessInputStream;
 import loci.common.xml.XMLTools;
 import loci.formats.CoreMetadata;
@@ -395,8 +396,8 @@ protected void initMetadataStore() throws FormatException {
         // Leica units are nanometres; convert to µm
         double sizeX = i.vSizeX / 1000.0;
         double sizeY = i.vSizeY / 1000.0;
-        final Length offsetX = new Length(i.vOffsetX, UNITS.NM);
-        final Length offsetY = new Length(i.vOffsetY, UNITS.NM);
+        final Length offsetX = new Length(i.vOffsetX, UNITS.NANOMETER);
+        final Length offsetY = new Length(i.vOffsetY, UNITS.NANOMETER);
         double sizeZ = i.vSpacingZ / 1000.0;
 
         store.setPixelsPhysicalSizeX(
@@ -422,7 +423,7 @@ protected void initMetadataStore() throws FormatException {
           Double mag = Double.parseDouble(i.objMag);
           store.setObjectiveNominalMagnification(mag, inst, objectiveidno);
           store.setObjectiveCalibratedMagnification(mag, inst, objectiveidno);
-          store.setObjectiveLensNA(new Double(i.illumNA), inst, objectiveidno);
+          store.setObjectiveLensNA(DataTools.parseDouble(i.illumNA), inst, objectiveidno);
           objectiveidno++;
         }
 
diff --git a/components/formats-gpl/src/loci/formats/in/LiFlimReader.java b/components/formats-gpl/src/loci/formats/in/LiFlimReader.java
index c3b5aaee6c2..828861b8095 100644
--- a/components/formats-gpl/src/loci/formats/in/LiFlimReader.java
+++ b/components/formats-gpl/src/loci/formats/in/LiFlimReader.java
@@ -390,7 +390,7 @@ else if (version.equals("2.0")){
           addGlobalMeta(metaKey, value);
 
           if (metaKey.startsWith(TIMESTAMP_KEY)) {
-            Integer index = new Integer(metaKey.replaceAll(TIMESTAMP_KEY, ""));
+            Integer index = Integer.parseInt(metaKey.replaceAll(TIMESTAMP_KEY, ""));
             stampValues.put(index, value);
           }
           else if (metaKey.equals("ROI: INFO - numregions")) {
@@ -401,7 +401,7 @@ else if (metaKey.startsWith("ROI: ROI") &&
           {
             int start = metaKey.lastIndexOf("ROI") + 3;
             int end = metaKey.indexOf(" ", start);
-            Integer index = new Integer(metaKey.substring(start, end));
+            Integer index = Integer.parseInt(metaKey.substring(start, end));
             ROI roi = rois.get(index);
             if (roi == null) roi = new ROI();
 
@@ -410,7 +410,7 @@ else if (metaKey.startsWith("ROI: ROI") &&
             }
             else if (metaKey.indexOf(" - p") >= 0) {
               String p = metaKey.substring(metaKey.indexOf(" - p") + 4);
-              roi.points.put(new Integer(p), value.replaceAll(" ", ","));
+              roi.points.put(Integer.parseInt(p), value.replaceAll(" ", ","));
             }
             rois.put(index, roi);
           }
@@ -423,7 +423,7 @@ else if (metaKey.equals("ExposureTime")) {
             } else {
               exposureTimeUnit = UNITS.SECOND;
             }
-            exposureTime = new Double(expTime);
+            exposureTime = Double.valueOf(expTime);
           }
         }
       }
@@ -567,7 +567,7 @@ private void initOMEMetadata() {
       }
       else {
         long ms = stamp - firstStamp;
-        deltaT = new Double(ms / 1000.0);
+        deltaT = Double.valueOf(ms / 1000.0);
       }
       for (int c=0; c<getEffectiveSizeC(); c++) {
         for (int z=0; z<getSizeZ(); z++) {
diff --git a/components/formats-gpl/src/loci/formats/in/MIASReader.java b/components/formats-gpl/src/loci/formats/in/MIASReader.java
index 49fa88efc05..8dfb4dde2a4 100644
--- a/components/formats-gpl/src/loci/formats/in/MIASReader.java
+++ b/components/formats-gpl/src/loci/formats/in/MIASReader.java
@@ -1026,8 +1026,8 @@ private void populateROI(List<String> columns, String[] data, int series,
     store.setEllipseID(MetadataTools.createLSID("Shape", roi, 0), roi, 0);
     store.setEllipseTheT(new NonNegativeInteger(time), roi, 0);
     store.setEllipseTheZ(new NonNegativeInteger(z), roi, 0);
-    store.setEllipseX(new Double(data[columns.indexOf("Col")]), roi, 0);
-    store.setEllipseY(new Double(data[columns.indexOf("Row")]), roi, 0);
+    store.setEllipseX(DataTools.parseDouble(data[columns.indexOf("Col")]), roi, 0);
+    store.setEllipseY(DataTools.parseDouble(data[columns.indexOf("Row")]), roi, 0);
     store.setEllipseText(data[columns.indexOf("Label")], roi, 0);
 
     double diam = Double.parseDouble(data[columns.indexOf("Cell Diam.")]);
@@ -1085,10 +1085,10 @@ else if (key.equals("Carrier")) {
           store.setPlateName(value, 0);
         }
         else if (key.equals("Pixel_X")) {
-          physicalSizeX = new Double(value);
+          physicalSizeX = DataTools.parseDouble(value);
         }
         else if (key.equals("Pixel_Y")) {
-          physicalSizeY = new Double(value);
+          physicalSizeY = DataTools.parseDouble(value);
         }
         else if (key.equals("Objective_ID")) {
           store.setObjectiveID(
@@ -1109,7 +1109,7 @@ else if (key.equals("Time")) {
           date += " " + value;
         }
         else if (key.equals("Exposure")) {
-          exposure = new Double(value);
+          exposure = DataTools.parseDouble(value);
         }
       }
     }
diff --git a/components/formats-gpl/src/loci/formats/in/MetamorphHandler.java b/components/formats-gpl/src/loci/formats/in/MetamorphHandler.java
index 8eff5190b52..e6bd7408ae3 100644
--- a/components/formats-gpl/src/loci/formats/in/MetamorphHandler.java
+++ b/components/formats-gpl/src/loci/formats/in/MetamorphHandler.java
@@ -256,7 +256,7 @@ else if (key.equals("stage-position-y")) {
       }
     }
     if (key.equals("wavelength")) {
-      wavelengths.add(new Integer(value));
+      wavelengths.add(Integer.parseInt(value));
     }
     else if (key.equals("acquisition-time-local")) {
       date = value;
diff --git a/components/formats-gpl/src/loci/formats/in/MetamorphReader.java b/components/formats-gpl/src/loci/formats/in/MetamorphReader.java
index 82b27902d0c..fa789935731 100644
--- a/components/formats-gpl/src/loci/formats/in/MetamorphReader.java
+++ b/components/formats-gpl/src/loci/formats/in/MetamorphReader.java
@@ -1170,7 +1170,7 @@ else if (commentEntry instanceof TiffIFDEntry) {
                     line.lastIndexOf("\"", lastQuote - 1) + 1, lastQuote);
 
                   if (key.equals("z-position")) {
-                    xmlZPosition = new Double(value);
+                    xmlZPosition = DataTools.parseDouble(value);
                   }
                   else if (key.equals("acquisition-time-local")) {
                     timestamps.add(value);
@@ -1473,7 +1473,7 @@ else if (key.equals("Gain")) {
                 nextSpace = value.length();
               }
               try {
-                gain = new Double(value.substring(space, nextSpace));
+                gain = DataTools.parseDouble(value.substring(space, nextSpace));
               }
               catch (NumberFormatException e) { }
             }
@@ -2004,13 +2004,13 @@ else if (valOrOffset == 0 && getSizeZ() < mmPlanes) {
         if (value instanceof TiffRational) {
           sizeX = ((TiffRational) value).doubleValue();
         }
-        else sizeX = new Double(value.toString());
+        else sizeX = DataTools.parseDouble(value.toString());
       }
       if ("YCalibration".equals(key) && value != null) {
         if (value instanceof TiffRational) {
           sizeY = ((TiffRational) value).doubleValue();
         }
-        else sizeY = new Double(value.toString());
+        else sizeY = DataTools.parseDouble(value.toString());
       }
     }
     in.seek(saveLoc);
diff --git a/components/formats-gpl/src/loci/formats/in/MicroCTReader.java b/components/formats-gpl/src/loci/formats/in/MicroCTReader.java
index ab3b5cac95d..490d7143be2 100644
--- a/components/formats-gpl/src/loci/formats/in/MicroCTReader.java
+++ b/components/formats-gpl/src/loci/formats/in/MicroCTReader.java
@@ -236,7 +236,7 @@ else if (key.equals("bits")) {
             ms.pixelType = FormatTools.pixelTypeFromBytes(bits / 8, true, false);
           }
           else if (key.equals("elementsize")) {
-            Double size = new Double(value);
+            Double size = DataTools.parseDouble(value);
             // physical size is stored in mm, not um
             physicalSize = new PositiveFloat(size * 1000);
           }
@@ -328,7 +328,7 @@ private void processKey(String key, String value) {
     addGlobalMeta(key, value);
 
     if (key.equals("Exposure Time (ms)")) {
-      exposureTime = new Double(value);
+      exposureTime = DataTools.parseDouble(value);
       exposureTime /= 1000.0;
     }
     else if (key.equals("Description.txt")) {
diff --git a/components/formats-gpl/src/loci/formats/in/ND2Handler.java b/components/formats-gpl/src/loci/formats/in/ND2Handler.java
index 53ec64c10cf..7a4dc80740f 100644
--- a/components/formats-gpl/src/loci/formats/in/ND2Handler.java
+++ b/components/formats-gpl/src/loci/formats/in/ND2Handler.java
@@ -154,7 +154,7 @@ public void populateROIs(MetadataStore store) {
           store.setLabelFontSize(new Length(fontSize, UNITS.POINT), r, 0);
         }
         store.setLabelText(roi.get("eval-text"), r, 0);
-        Length l = new Length(new Double(roi.get("line-width")), UNITS.PIXEL);
+        Length l = new Length(DataTools.parseDouble(roi.get("line-width")), UNITS.PIXEL);
         store.setLabelStrokeWidth(l, r, 0);
 
         String rectangle = roi.get("rectangle");
@@ -568,7 +568,7 @@ else if (qName.equals("dPinholeRadius")) {
       }
       else if (qName.endsWith("ChannelColor")) {
         String name = qName.substring(0, qName.indexOf("Channel"));
-        colors.put(name, new Integer(value));
+        colors.put(name, Integer.parseInt(value));
       }
       else if (qName.endsWith("DyeName")) {
         int channelIndex = qName.indexOf("Channel");
@@ -885,11 +885,11 @@ else if (key.equals("Line")) {
       }
       else if (key.equalsIgnoreCase("Emission wavelength")) {
         String[] v = value.split(" ");
-        emWave.add(new Double(v[0]));
+        emWave.add(DataTools.parseDouble(v[0]));
       }
       else if (key.equalsIgnoreCase("Excitation wavelength")) {
         String[] v = value.split(" ");
-        exWave.add(new Double(v[0]));
+        exWave.add(DataTools.parseDouble(v[0]));
       }
       else if (key.equals("Power")) {
         power.add(DataTools.parseDouble(value).intValue());
@@ -898,7 +898,10 @@ else if (key.equals("CameraUniqueName")) {
         cameraModel = value;
       }
       else if (key.equals("ExposureTime")) {
-        exposureTime.add(new Double(value) / 1000d);
+        Double time = DataTools.parseDouble(value);
+        if (time != null) {
+          exposureTime.add(time / 1000d);
+        }
       }
       else if (key.equals("sDate")) {
         date = DateTools.formatDate(value, DATE_FORMAT);
diff --git a/components/formats-gpl/src/loci/formats/in/ND2Reader.java b/components/formats-gpl/src/loci/formats/in/ND2Reader.java
index 01e7ce6ccdd..77b03b0cc64 100644
--- a/components/formats-gpl/src/loci/formats/in/ND2Reader.java
+++ b/components/formats-gpl/src/loci/formats/in/ND2Reader.java
@@ -713,7 +713,7 @@ else if (trueSizeY == 0) {
 
               lastImage = entry;
 
-              imageOffsets.add(new Long(entry.position + 16));
+              imageOffsets.add(Long.valueOf(entry.position + 16));
               int realLength = (int) Math.max(entry.name.length() + 1, nameLength);
               imageLengths.add(new long[] {realLength, entry.length - nameLength - 16, getSizeX() * getSizeY()});
               imageNames.add(entry.name.substring(12));
@@ -2188,7 +2188,7 @@ private ArrayList<String> iterateIn(RandomAccessInputStream in, Long stop, boole
         name = name.trim();
 
         if (name.equals("bUseZ")) {
-          useZ = new Boolean(value.toString());
+          useZ = Boolean.parseBoolean(value.toString());
         }
         else if (name.equals("sDescription")) {
           if (currentColor != null) {
@@ -2209,7 +2209,7 @@ else if (name.equals("EmWavelength")) {
           textEmissionWavelengths.add(wave);
         }
         else if (name.equals("dZStep")) {
-          trueSizeZ = new Double(value.toString());
+          trueSizeZ = DataTools.parseDouble(value.toString());
         }
         else if (name.equals("dZHigh")) {
           zHigh = DataTools.parseDouble(value.toString());
diff --git a/components/formats-gpl/src/loci/formats/in/NDPIReader.java b/components/formats-gpl/src/loci/formats/in/NDPIReader.java
index 32fc44d20df..b17548bf03c 100644
--- a/components/formats-gpl/src/loci/formats/in/NDPIReader.java
+++ b/components/formats-gpl/src/loci/formats/in/NDPIReader.java
@@ -551,7 +551,7 @@ else if (s < pyramidHeight) {
 
         // key name not a typo
         if (key.equals("Objective.Lens.Magnificant") && magnification == null) {
-          magnification = new Double(value);
+          magnification = DataTools.parseDouble(value);
         }
         else if (key.equals("NDP.S/N")) {
           serialNumber = value;
diff --git a/components/formats-gpl/src/loci/formats/in/NiftiReader.java b/components/formats-gpl/src/loci/formats/in/NiftiReader.java
index b353b0d6171..7373933c23a 100644
--- a/components/formats-gpl/src/loci/formats/in/NiftiReader.java
+++ b/components/formats-gpl/src/loci/formats/in/NiftiReader.java
@@ -303,11 +303,11 @@ else if (checkSuffix(id, "nii")) {
       store.setImageDescription(description, 0);
 
       Length sizeX =
-        FormatTools.getPhysicalSizeX(new Double(voxelWidth), spatialUnit);
+        FormatTools.getPhysicalSizeX(Double.valueOf(voxelWidth), spatialUnit);
       Length sizeY =
-        FormatTools.getPhysicalSizeY(new Double(voxelHeight), spatialUnit);
+        FormatTools.getPhysicalSizeY(Double.valueOf(voxelHeight), spatialUnit);
       Length sizeZ =
-        FormatTools.getPhysicalSizeZ(new Double(sliceThickness), spatialUnit);
+        FormatTools.getPhysicalSizeZ(Double.valueOf(sliceThickness), spatialUnit);
 
       if (sizeX != null) {
         store.setPixelsPhysicalSizeX(sizeX, 0);
@@ -318,7 +318,7 @@ else if (checkSuffix(id, "nii")) {
       if (sizeZ != null) {
         store.setPixelsPhysicalSizeZ(sizeZ, 0);
       }
-      store.setPixelsTimeIncrement(new Time(new Double(deltaT), timeUnit), 0);
+      store.setPixelsTimeIncrement(new Time(Double.valueOf(deltaT), timeUnit), 0);
     }
   }
 
diff --git a/components/formats-gpl/src/loci/formats/in/NikonTiffReader.java b/components/formats-gpl/src/loci/formats/in/NikonTiffReader.java
index 94f70bde608..737f282bcd6 100644
--- a/components/formats-gpl/src/loci/formats/in/NikonTiffReader.java
+++ b/components/formats-gpl/src/loci/formats/in/NikonTiffReader.java
@@ -29,6 +29,7 @@
 import java.util.ArrayList;
 import java.util.List;
 
+import loci.common.DataTools;
 import loci.common.RandomAccessInputStream;
 import loci.formats.FormatException;
 import loci.formats.FormatTools;
@@ -167,7 +168,7 @@ else if (key.equals("history objective Type")) {
         correction = value;
       }
       else if (key.equals("history objective Magnification")) {
-        magnification = new Double(value);
+        magnification = DataTools.parseDouble(value);
       }
       else if (key.equals("history objective NA")) {
         lensNA = Double.parseDouble(value);
@@ -179,25 +180,25 @@ else if (key.equals("history objective Immersion")) {
         immersion = value;
       }
       else if (key.startsWith("history gain")) {
-        gain.add(new Double(value));
+        gain.add(DataTools.parseDouble(value));
       }
       else if (key.equals("history pinhole")) {
-        pinholeSize = new Double(value.substring(0, value.indexOf(' ')));
+        pinholeSize = DataTools.parseDouble(value.substring(0, value.indexOf(' ')));
       }
       else if (key.startsWith("history laser") && key.endsWith("wavelength")) {
-        wavelength.add(new Double(value.replaceAll("\\D", "")));
+        wavelength.add(DataTools.parseDouble(value.replaceAll("\\D", "")));
       }
       else if (key.startsWith("history laser") && key.endsWith("name")) {
         laserIDs.add(value);
       }
       else if (key.equals("sensor s_params LambdaEx")) {
         for (int i=nTokensInKey; i<tokens.length; i++) {
-          exWave.add(new Double(tokens[i]));
+          exWave.add(DataTools.parseDouble(tokens[i]));
         }
       }
       else if (key.equals("sensor s_params LambdaEm")) {
         for (int i=nTokensInKey; i<tokens.length; i++) {
-          emWave.add(new Double(tokens[i]));
+          emWave.add(DataTools.parseDouble(tokens[i]));
         }
       }
 
diff --git a/components/formats-gpl/src/loci/formats/in/OIRReader.java b/components/formats-gpl/src/loci/formats/in/OIRReader.java
index 71e3a4ee3b7..a432b0d6c8c 100644
--- a/components/formats-gpl/src/loci/formats/in/OIRReader.java
+++ b/components/formats-gpl/src/loci/formats/in/OIRReader.java
@@ -419,8 +419,8 @@ public int compare(String s1, String s2) {
         int lastUnderscore1 = s1.lastIndexOf("_");
         int lastUnderscore2 = s2.lastIndexOf("_");
 
-        Integer block1 = new Integer(s1.substring(lastUnderscore1 + 1));
-        Integer block2 = new Integer(s2.substring(lastUnderscore2 + 1));
+        Integer block1 = Integer.parseInt(s1.substring(lastUnderscore1 + 1));
+        Integer block2 = Integer.parseInt(s2.substring(lastUnderscore2 + 1));
 
         int underscore1 = s1.lastIndexOf("_", lastUnderscore1 - 1);
         int underscore2 = s2.lastIndexOf("_", lastUnderscore2 - 1);
diff --git a/components/formats-gpl/src/loci/formats/in/OlympusTileReader.java b/components/formats-gpl/src/loci/formats/in/OlympusTileReader.java
index 0a1152cf658..b4a5191a4a6 100644
--- a/components/formats-gpl/src/loci/formats/in/OlympusTileReader.java
+++ b/components/formats-gpl/src/loci/formats/in/OlympusTileReader.java
@@ -295,8 +295,8 @@ else if (checkSuffix(tileFile, "vsi")) {
         int diffY = stageOverlap * rows * 4;
 
         if (stitchedWidth != null && stitchedHeight != null) {
-          int actualWidth = (int) (stitchedWidth / physicalSizeX.value(UNITS.NM).doubleValue());
-          int actualHeight = (int) (stitchedHeight / physicalSizeY.value(UNITS.NM).doubleValue());
+          int actualWidth = (int) (stitchedWidth / physicalSizeX.value(UNITS.NANOMETER).doubleValue());
+          int actualHeight = (int) (stitchedHeight / physicalSizeY.value(UNITS.NANOMETER).doubleValue());
 
           diffX = widthWithOverlaps - actualWidth;
           diffY = heightWithOverlaps - actualHeight;
diff --git a/components/formats-gpl/src/loci/formats/in/OpenlabReader.java b/components/formats-gpl/src/loci/formats/in/OpenlabReader.java
index edfe7da01cf..d5484891333 100644
--- a/components/formats-gpl/src/loci/formats/in/OpenlabReader.java
+++ b/components/formats-gpl/src/loci/formats/in/OpenlabReader.java
@@ -30,6 +30,7 @@
 import java.util.List;
 
 import loci.common.ByteArrayHandle;
+import loci.common.DataTools;
 import loci.common.Location;
 import loci.common.RandomAccessInputStream;
 import loci.formats.ChannelSeparator;
@@ -597,8 +598,8 @@ else if (tag == USER) {
     if (level != MetadataLevel.MINIMUM) {
       // populate MetadataStore
 
-      Length sizeX = FormatTools.getPhysicalSizeX(new Double(xcal));
-      Length sizeY = FormatTools.getPhysicalSizeY(new Double(ycal));
+      Length sizeX = FormatTools.getPhysicalSizeX(Double.valueOf(xcal));
+      Length sizeY = FormatTools.getPhysicalSizeY(Double.valueOf(ycal));
 
       if (sizeX != null) {
         store.setPixelsPhysicalSizeX(sizeX, 0);
@@ -614,13 +615,13 @@ else if (tag == USER) {
 
       try {
         if (gain != null) {
-          store.setDetectorSettingsGain(new Double(gain), 0, 0);
+          store.setDetectorSettingsGain(DataTools.parseDouble(gain), 0, 0);
         }
       }
       catch (NumberFormatException e) { }
       try {
         if (detectorOffset != null) {
-          store.setDetectorSettingsOffset(new Double(detectorOffset), 0, 0);
+          store.setDetectorSettingsOffset(DataTools.parseDouble(detectorOffset), 0, 0);
         }
       }
       catch (NumberFormatException e) { }
diff --git a/components/formats-gpl/src/loci/formats/in/OperettaReader.java b/components/formats-gpl/src/loci/formats/in/OperettaReader.java
index 305eabe3ad6..15db568d5ab 100644
--- a/components/formats-gpl/src/loci/formats/in/OperettaReader.java
+++ b/components/formats-gpl/src/loci/formats/in/OperettaReader.java
@@ -1199,6 +1199,7 @@ else if (emWavelength < 610) {
   }
 
   @Override
+  @Deprecated
   protected AcquisitionMode getAcquisitionMode(String mode) throws FormatException {
     if (mode == null) {
       return null;
diff --git a/components/formats-gpl/src/loci/formats/in/PCORAWReader.java b/components/formats-gpl/src/loci/formats/in/PCORAWReader.java
index a4172d68529..19630ca92a6 100644
--- a/components/formats-gpl/src/loci/formats/in/PCORAWReader.java
+++ b/components/formats-gpl/src/loci/formats/in/PCORAWReader.java
@@ -208,7 +208,7 @@ protected void initFile(String id) throws FormatException, IOException {
           // set the exposure time
 
           String exp = value.substring(0, value.indexOf(' '));
-          Double parsedExp = new Double(exp);
+          Double parsedExp = DataTools.parseDouble(exp);
           Time exposure = null;
           if (parsedExp != null) {
             exposure = new Time(parsedExp / 1000, UNITS.SECOND);
diff --git a/components/formats-gpl/src/loci/formats/in/PDSReader.java b/components/formats-gpl/src/loci/formats/in/PDSReader.java
index 8ebd371110c..8ad93d0d9e2 100644
--- a/components/formats-gpl/src/loci/formats/in/PDSReader.java
+++ b/components/formats-gpl/src/loci/formats/in/PDSReader.java
@@ -234,10 +234,10 @@ else if (key.equals("SIGNY")) {
         reverseY = value.replaceAll("'", "").trim().equals("-");
       }
       else if (key.equals("DELTAX")) {
-        deltaX = new Double(value);
+        deltaX = DataTools.parseDouble(value);
       }
       else if (key.equals("DELTAY")) {
-        deltaY = new Double(value);
+        deltaY = DataTools.parseDouble(value);
       }
       else if (key.equals("COLOR")) {
         int color = Integer.parseInt(value);
diff --git a/components/formats-gpl/src/loci/formats/in/PerkinElmerReader.java b/components/formats-gpl/src/loci/formats/in/PerkinElmerReader.java
index d960c6c169a..35f2960bfd8 100644
--- a/components/formats-gpl/src/loci/formats/in/PerkinElmerReader.java
+++ b/components/formats-gpl/src/loci/formats/in/PerkinElmerReader.java
@@ -489,7 +489,7 @@ protected void initFile(String id) throws FormatException, IOException {
           if (exposure.endsWith(",")) {
             exposure = exposure.substring(0, exposure.length() - 1);
           }
-          exposureTimes.add(new Double(Double.parseDouble(exposure) / 1000));
+          exposureTimes.add(Double.parseDouble(exposure) / 1000);
 
           if (tokens[j].indexOf("nm") != -1) {
             int nmIndex = tokens[j].indexOf("nm");
@@ -497,14 +497,14 @@ protected void initFile(String id) throws FormatException, IOException {
             int slash = tokens[j].lastIndexOf("/", nmIndex);
             if (slash == -1) slash = nmIndex;
             emWaves.add(
-              new Double(tokens[j].substring(paren + 1, slash).trim()));
+              DataTools.parseDouble(tokens[j].substring(paren + 1, slash).trim()));
             if (tokens[j].indexOf("nm", nmIndex + 3) != -1) {
               nmIndex = tokens[j].indexOf("nm", nmIndex + 3);
               paren = tokens[j].lastIndexOf(" ", nmIndex);
               slash = tokens[j].lastIndexOf("/", nmIndex);
               if (slash == -1) slash = nmIndex + 2;
               exWaves.add(
-                new Double(tokens[j].substring(paren + 1, slash).trim()));
+                DataTools.parseDouble(tokens[j].substring(paren + 1, slash).trim()));
             }
           }
 
@@ -514,7 +514,7 @@ else if (tokens[j + 1].trim().equals("Slice Z positions")) {
           for (int q=j + 2; q<tokens.length; q++) {
             if (!tokens[q].trim().equals("")) {
               try {
-                zPositions.add(new Double(tokens[q].trim()));
+                zPositions.add(DataTools.parseDouble(tokens[q].trim()));
               }
               catch (NumberFormatException e) { }
             }
diff --git a/components/formats-gpl/src/loci/formats/in/PrairieMetadata.java b/components/formats-gpl/src/loci/formats/in/PrairieMetadata.java
index ffe47ace448..00a5daf5939 100644
--- a/components/formats-gpl/src/loci/formats/in/PrairieMetadata.java
+++ b/components/formats-gpl/src/loci/formats/in/PrairieMetadata.java
@@ -32,6 +32,8 @@
 import java.util.HashSet;
 import java.util.Map;
 
+import loci.common.DataTools;
+
 import ome.units.UNITS;
 import ome.units.quantity.Length;
 
@@ -492,7 +494,7 @@ private boolean b(final String value) {
   private Double d(final String value) {
     if (value == null) return null;
     try {
-      return new Double(value);
+      return DataTools.parseDouble(value);
     }
     catch (final NumberFormatException exc) {
       // TODO: log it
@@ -506,7 +508,7 @@ private Double d(final String value) {
   private Integer i(final String value) {
     if (value == null) return null;
     try {
-      return new Integer(value);
+      return Integer.parseInt(value);
     }
     catch (final NumberFormatException exc) {
       // TODO: log it
diff --git a/components/formats-gpl/src/loci/formats/in/PrairieReader.java b/components/formats-gpl/src/loci/formats/in/PrairieReader.java
index 563e9ab436e..bdaae459d7c 100644
--- a/components/formats-gpl/src/loci/formats/in/PrairieReader.java
+++ b/components/formats-gpl/src/loci/formats/in/PrairieReader.java
@@ -198,9 +198,9 @@ public boolean isThisType(RandomAccessInputStream stream) throws IOException {
     }
     if (software == null) return false;
     if (software.indexOf("Prairie") < 0) return false; // not Prairie software
-    return ifd.containsKey(new Integer(PRAIRIE_TAG_1)) &&
-      ifd.containsKey(new Integer(PRAIRIE_TAG_2)) &&
-      ifd.containsKey(new Integer(PRAIRIE_TAG_3));
+    return ifd.containsKey(Integer.valueOf(PRAIRIE_TAG_1)) &&
+      ifd.containsKey(Integer.valueOf(PRAIRIE_TAG_2)) &&
+      ifd.containsKey(Integer.valueOf(PRAIRIE_TAG_3));
   }
 
   @Override
diff --git a/components/formats-gpl/src/loci/formats/in/SBIGReader.java b/components/formats-gpl/src/loci/formats/in/SBIGReader.java
index 531589e8269..01ad8f74f30 100644
--- a/components/formats-gpl/src/loci/formats/in/SBIGReader.java
+++ b/components/formats-gpl/src/loci/formats/in/SBIGReader.java
@@ -160,10 +160,16 @@ else if (key.equals("Note")) {
           description = value;
         }
         else if (key.equals("X_pixel_size")) {
-          sizeX = new Double(value) * 1000;
+          Double size = DataTools.parseDouble(value);
+          if (size != null) {
+            sizeX = size * 1000;
+          }
         }
         else if (key.equals("Y_pixel_size")) {
-          sizeY = new Double(value) * 1000;
+          Double size = DataTools.parseDouble(value);
+          if (size != null) {
+            sizeY = size * 1000;
+          }
         }
         else if (key.equals("Date")) {
           date = value;
diff --git a/components/formats-gpl/src/loci/formats/in/SDTInfo.java b/components/formats-gpl/src/loci/formats/in/SDTInfo.java
index 1e9f81ac253..8dfa24f227f 100644
--- a/components/formats-gpl/src/loci/formats/in/SDTInfo.java
+++ b/components/formats-gpl/src/loci/formats/in/SDTInfo.java
@@ -458,24 +458,24 @@ public SDTInfo(RandomAccessInputStream in, Hashtable meta)
     // save bhfileHeader to metadata table
     if (meta != null) {
       final String bhfileHeader = "bhfileHeader.";
-      meta.put(bhfileHeader + "revision", new Short(revision));
-      meta.put(bhfileHeader + "infoOffs", new Integer(infoOffs));
-      meta.put(bhfileHeader + "infoLength", new Short(infoLength));
-      meta.put(bhfileHeader + "setupOffs", new Integer(setupOffs));
-      meta.put(bhfileHeader + "dataBlockOffs", new Integer(dataBlockOffs));
-      meta.put(bhfileHeader + "noOfDataBlocks", new Short(noOfDataBlocks));
+      meta.put(bhfileHeader + "revision", Short.valueOf(revision));
+      meta.put(bhfileHeader + "infoOffs", Integer.valueOf(infoOffs));
+      meta.put(bhfileHeader + "infoLength", Short.valueOf(infoLength));
+      meta.put(bhfileHeader + "setupOffs", Integer.valueOf(setupOffs));
+      meta.put(bhfileHeader + "dataBlockOffs", Integer.valueOf(dataBlockOffs));
+      meta.put(bhfileHeader + "noOfDataBlocks", Short.valueOf(noOfDataBlocks));
       meta.put(bhfileHeader + "dataBlockLength",
-        new Integer(dataBlockLength));
+        Integer.valueOf(dataBlockLength));
       meta.put(bhfileHeader + "measDescBlockOffs",
-        new Integer(measDescBlockOffs));
+        Integer.valueOf(measDescBlockOffs));
       meta.put(bhfileHeader + "noOfMeasDescBlocks",
-        new Short(noOfMeasDescBlocks));
+        Short.valueOf(noOfMeasDescBlocks));
       meta.put(bhfileHeader + "measDescBlockLength",
-        new Integer(measDescBlockLength));
-      meta.put(bhfileHeader + "headerValid", new Integer(headerValid));
-      meta.put(bhfileHeader + "reserved1", new Long(reserved1));
-      meta.put(bhfileHeader + "reserved2", new Integer(reserved2));
-      meta.put(bhfileHeader + "chksum", new Integer(chksum));
+        Integer.valueOf(measDescBlockLength));
+      meta.put(bhfileHeader + "headerValid", Integer.valueOf(headerValid));
+      meta.put(bhfileHeader + "reserved1", Long.valueOf(reserved1));
+      meta.put(bhfileHeader + "reserved2", Integer.valueOf(reserved2));
+      meta.put(bhfileHeader + "chksum", Integer.valueOf(chksum));
     }
 
     // read file info
@@ -716,61 +716,61 @@ else if (token.indexOf(Y_IMG_STRING) != -1) {
           meta.put(measureInfo + "time", time);
           meta.put(measureInfo + "date", date);
           meta.put(measureInfo + "modSerNo", modSerNo);
-          meta.put(measureInfo + "measMode", new Short(measMode));
-          meta.put(measureInfo + "cfdLL", new Float(cfdLL));
-          meta.put(measureInfo + "cfdLH", new Float(cfdLH));
-          meta.put(measureInfo + "cfdZC", new Float(cfdZC));
-          meta.put(measureInfo + "cfdHF", new Float(cfdHF));
-          meta.put(measureInfo + "synZC", new Float(synZC));
-          meta.put(measureInfo + "synFD", new Short(synFD));
-          meta.put(measureInfo + "synHF", new Float(synHF));
-          meta.put(measureInfo + "tacR", new Float(tacR));
-          meta.put(measureInfo + "tacG", new Short(tacG));
-          meta.put(measureInfo + "tacOF", new Float(tacOF));
-          meta.put(measureInfo + "tacLL", new Float(tacLL));
-          meta.put(measureInfo + "tacLH", new Float(tacLH));
-          meta.put(measureInfo + "adcRE", new Short(adcRE));
-          meta.put(measureInfo + "ealDE", new Short(ealDE));
-          meta.put(measureInfo + "ncx", new Short(ncx));
-          meta.put(measureInfo + "ncy", new Short(ncy));
-          meta.put(measureInfo + "page", new Integer(page));
-          meta.put(measureInfo + "colT", new Float(colT));
-          meta.put(measureInfo + "repT", new Float(repT));
-          meta.put(measureInfo + "stopt", new Short(stopt));
-          meta.put(measureInfo + "overfl", new Integer(overfl));
-          meta.put(measureInfo + "useMotor", new Short(useMotor));
-          meta.put(measureInfo + "steps", new Integer(steps));
-          meta.put(measureInfo + "offset", new Float(offset));
-          meta.put(measureInfo + "dither", new Short(dither));
-          meta.put(measureInfo + "incr", new Short(incr));
-          meta.put(measureInfo + "memBank", new Short(memBank));
+          meta.put(measureInfo + "measMode", Short.valueOf(measMode));
+          meta.put(measureInfo + "cfdLL", Float.valueOf(cfdLL));
+          meta.put(measureInfo + "cfdLH", Float.valueOf(cfdLH));
+          meta.put(measureInfo + "cfdZC", Float.valueOf(cfdZC));
+          meta.put(measureInfo + "cfdHF", Float.valueOf(cfdHF));
+          meta.put(measureInfo + "synZC", Float.valueOf(synZC));
+          meta.put(measureInfo + "synFD", Short.valueOf(synFD));
+          meta.put(measureInfo + "synHF", Float.valueOf(synHF));
+          meta.put(measureInfo + "tacR", Float.valueOf(tacR));
+          meta.put(measureInfo + "tacG", Short.valueOf(tacG));
+          meta.put(measureInfo + "tacOF", Float.valueOf(tacOF));
+          meta.put(measureInfo + "tacLL", Float.valueOf(tacLL));
+          meta.put(measureInfo + "tacLH", Float.valueOf(tacLH));
+          meta.put(measureInfo + "adcRE", Short.valueOf(adcRE));
+          meta.put(measureInfo + "ealDE", Short.valueOf(ealDE));
+          meta.put(measureInfo + "ncx", Short.valueOf(ncx));
+          meta.put(measureInfo + "ncy", Short.valueOf(ncy));
+          meta.put(measureInfo + "page", Integer.valueOf(page));
+          meta.put(measureInfo + "colT", Float.valueOf(colT));
+          meta.put(measureInfo + "repT", Float.valueOf(repT));
+          meta.put(measureInfo + "stopt", Short.valueOf(stopt));
+          meta.put(measureInfo + "overfl", Integer.valueOf(overfl));
+          meta.put(measureInfo + "useMotor", Short.valueOf(useMotor));
+          meta.put(measureInfo + "steps", Integer.valueOf(steps));
+          meta.put(measureInfo + "offset", Float.valueOf(offset));
+          meta.put(measureInfo + "dither", Short.valueOf(dither));
+          meta.put(measureInfo + "incr", Short.valueOf(incr));
+          meta.put(measureInfo + "memBank", Short.valueOf(memBank));
           meta.put(measureInfo + "modType", modType);
-          meta.put(measureInfo + "synTH", new Float(synTH));
-          meta.put(measureInfo + "deadTimeComp", new Short(deadTimeComp));
-          meta.put(measureInfo + "polarityL", new Short(polarityL));
-          meta.put(measureInfo + "polarityF", new Short(polarityF));
-          meta.put(measureInfo + "polarityP", new Short(polarityP));
-          meta.put(measureInfo + "linediv", new Short(linediv));
-          meta.put(measureInfo + "accumulate", new Short(accumulate));
-          meta.put(measureInfo + "flbckY", new Integer(flbckY));
-          meta.put(measureInfo + "flbckX", new Integer(flbckX));
-          meta.put(measureInfo + "bordU", new Integer(bordU));
-          meta.put(measureInfo + "bordL", new Integer(bordL));
-          meta.put(measureInfo + "pixTime", new Float(pixTime));
-          meta.put(measureInfo + "pixClk", new Short(pixClk));
-          meta.put(measureInfo + "trigger", new Short(trigger));
-          meta.put(measureInfo + "scanX", new Integer(scanX));
-          meta.put(measureInfo + "scanY", new Integer(scanY));
-          meta.put(measureInfo + "scanRX", new Integer(scanRX));
-          meta.put(measureInfo + "scanRY", new Integer(scanRY));
-          meta.put(measureInfo + "fifoTyp", new Short(fifoTyp));
-          meta.put(measureInfo + "epxDiv", new Integer(epxDiv));
-          meta.put(measureInfo + "modTypeCode", new Integer(modTypeCode));
-          meta.put(measureInfo + "modFpgaVer", new Integer(modFpgaVer));
+          meta.put(measureInfo + "synTH", Float.valueOf(synTH));
+          meta.put(measureInfo + "deadTimeComp", Short.valueOf(deadTimeComp));
+          meta.put(measureInfo + "polarityL", Short.valueOf(polarityL));
+          meta.put(measureInfo + "polarityF", Short.valueOf(polarityF));
+          meta.put(measureInfo + "polarityP", Short.valueOf(polarityP));
+          meta.put(measureInfo + "linediv", Short.valueOf(linediv));
+          meta.put(measureInfo + "accumulate", Short.valueOf(accumulate));
+          meta.put(measureInfo + "flbckY", Integer.valueOf(flbckY));
+          meta.put(measureInfo + "flbckX", Integer.valueOf(flbckX));
+          meta.put(measureInfo + "bordU", Integer.valueOf(bordU));
+          meta.put(measureInfo + "bordL", Integer.valueOf(bordL));
+          meta.put(measureInfo + "pixTime", Float.valueOf(pixTime));
+          meta.put(measureInfo + "pixClk", Short.valueOf(pixClk));
+          meta.put(measureInfo + "trigger", Short.valueOf(trigger));
+          meta.put(measureInfo + "scanX", Integer.valueOf(scanX));
+          meta.put(measureInfo + "scanY", Integer.valueOf(scanY));
+          meta.put(measureInfo + "scanRX", Integer.valueOf(scanRX));
+          meta.put(measureInfo + "scanRY", Integer.valueOf(scanRY));
+          meta.put(measureInfo + "fifoTyp", Short.valueOf(fifoTyp));
+          meta.put(measureInfo + "epxDiv", Integer.valueOf(epxDiv));
+          meta.put(measureInfo + "modTypeCode", Integer.valueOf(modTypeCode));
+          meta.put(measureInfo + "modFpgaVer", Integer.valueOf(modFpgaVer));
           meta.put(measureInfo + "overflowCorrFactor",
-            new Float(overflowCorrFactor));
-          meta.put(measureInfo + "adcZoom", new Integer(adcZoom));
-          meta.put(measureInfo + "cycles", new Integer(cycles));
+            Float.valueOf(overflowCorrFactor));
+          meta.put(measureInfo + "adcZoom", Integer.valueOf(adcZoom));
+          meta.put(measureInfo + "cycles", Integer.valueOf(cycles));
         }
 
         // extract dimensional parameters from measure info
@@ -817,22 +817,22 @@ else if (token.indexOf(Y_IMG_STRING) != -1) {
         // save MeasStopInfo to metadata table
         if (meta != null) {
           final String measStopInfo = "MeasStopInfo.";
-          meta.put(measStopInfo + "status", new Integer(status));
-          meta.put(measStopInfo + "flags", new Integer(flags));
-          meta.put(measStopInfo + "stopTime", new Float(stopTime));
-          meta.put(measStopInfo + "curStep", new Integer(curStep));
-          meta.put(measStopInfo + "curCycle", new Integer(curCycle));
-          meta.put(measStopInfo + "curPage", new Integer(curPage));
-          meta.put(measStopInfo + "minSyncRate", new Float(minSyncRate));
-          meta.put(measStopInfo + "minCfdRate", new Float(minCfdRate));
-          meta.put(measStopInfo + "minTacRate", new Float(minTacRate));
-          meta.put(measStopInfo + "minAdcRate", new Float(minAdcRate));
-          meta.put(measStopInfo + "maxSyncRate", new Float(maxSyncRate));
-          meta.put(measStopInfo + "maxCfdRate", new Float(maxCfdRate));
-          meta.put(measStopInfo + "maxTacRate", new Float(maxTacRate));
-          meta.put(measStopInfo + "maxAdcRate", new Float(maxAdcRate));
-          meta.put(measStopInfo + "reserved1", new Integer(mReserved1));
-          meta.put(measStopInfo + "reserved2", new Float(mReserved2));
+          meta.put(measStopInfo + "status", Integer.valueOf(status));
+          meta.put(measStopInfo + "flags", Integer.valueOf(flags));
+          meta.put(measStopInfo + "stopTime", Float.valueOf(stopTime));
+          meta.put(measStopInfo + "curStep", Integer.valueOf(curStep));
+          meta.put(measStopInfo + "curCycle", Integer.valueOf(curCycle));
+          meta.put(measStopInfo + "curPage", Integer.valueOf(curPage));
+          meta.put(measStopInfo + "minSyncRate", Float.valueOf(minSyncRate));
+          meta.put(measStopInfo + "minCfdRate", Float.valueOf(minCfdRate));
+          meta.put(measStopInfo + "minTacRate", Float.valueOf(minTacRate));
+          meta.put(measStopInfo + "minAdcRate", Float.valueOf(minAdcRate));
+          meta.put(measStopInfo + "maxSyncRate", Float.valueOf(maxSyncRate));
+          meta.put(measStopInfo + "maxCfdRate", Float.valueOf(maxCfdRate));
+          meta.put(measStopInfo + "maxTacRate", Float.valueOf(maxTacRate));
+          meta.put(measStopInfo + "maxAdcRate", Float.valueOf(maxAdcRate));
+          meta.put(measStopInfo + "reserved1", Integer.valueOf(mReserved1));
+          meta.put(measStopInfo + "reserved2", Float.valueOf(mReserved2));
         }
       }
 
@@ -855,19 +855,19 @@ else if (token.indexOf(Y_IMG_STRING) != -1) {
         // save MeasFCSInfo to metadata table
         if (meta != null) {
           final String measFCSInfo = "MeasFCSInfo.";
-          meta.put(measFCSInfo + "chan", new Integer(chan));
-          meta.put(measFCSInfo + "fcsDecayCalc", new Integer(fcsDecayCalc));
-          meta.put(measFCSInfo + "mtResol", new Long(mtResol));
-          meta.put(measFCSInfo + "cortime", new Float(cortime));
-          meta.put(measFCSInfo + "calcPhotons", new Long(calcPhotons));
-          meta.put(measFCSInfo + "fcsPoints", new Integer(fcsPoints));
-          meta.put(measFCSInfo + "endTime", new Float(endTime));
-          meta.put(measFCSInfo + "overruns", new Integer(overruns));
-          meta.put(measFCSInfo + "fcsType", new Integer(fcsType));
-          meta.put(measFCSInfo + "crossChan", new Integer(crossChan));
-          meta.put(measFCSInfo + "mod", new Integer(mod));
-          meta.put(measFCSInfo + "crossMod", new Integer(crossMod));
-          meta.put(measFCSInfo + "crossMtResol", new Float(crossMtResol));
+          meta.put(measFCSInfo + "chan", Integer.valueOf(chan));
+          meta.put(measFCSInfo + "fcsDecayCalc", Integer.valueOf(fcsDecayCalc));
+          meta.put(measFCSInfo + "mtResol", Long.valueOf(mtResol));
+          meta.put(measFCSInfo + "cortime", Float.valueOf(cortime));
+          meta.put(measFCSInfo + "calcPhotons", Long.valueOf(calcPhotons));
+          meta.put(measFCSInfo + "fcsPoints", Integer.valueOf(fcsPoints));
+          meta.put(measFCSInfo + "endTime", Float.valueOf(endTime));
+          meta.put(measFCSInfo + "overruns", Integer.valueOf(overruns));
+          meta.put(measFCSInfo + "fcsType", Integer.valueOf(fcsType));
+          meta.put(measFCSInfo + "crossChan", Integer.valueOf(crossChan));
+          meta.put(measFCSInfo + "mod", Integer.valueOf(mod));
+          meta.put(measFCSInfo + "crossMod", Integer.valueOf(crossMod));
+          meta.put(measFCSInfo + "crossMtResol", Float.valueOf(crossMtResol));
         }
       }
 
@@ -885,15 +885,15 @@ else if (token.indexOf(Y_IMG_STRING) != -1) {
         // save extra MeasureInfo to metadata table
         if (meta != null) {
           final String measureInfo = "MeasureInfo.";
-          meta.put(measureInfo + "imageX", new Integer(imageX));
-          meta.put(measureInfo + "imageY", new Integer(imageY));
-          meta.put(measureInfo + "imageRX", new Integer(imageRX));
-          meta.put(measureInfo + "imageRY", new Integer(imageRY));
-          meta.put(measureInfo + "xyGain", new Short(xyGain));
-          meta.put(measureInfo + "masterClock", new Short(masterClock));
-          meta.put(measureInfo + "adcDE", new Short(adcDE));
-          meta.put(measureInfo + "detType", new Short(detType));
-          meta.put(measureInfo + "xAxis", new Short(xAxis));
+          meta.put(measureInfo + "imageX", Integer.valueOf(imageX));
+          meta.put(measureInfo + "imageY", Integer.valueOf(imageY));
+          meta.put(measureInfo + "imageRX", Integer.valueOf(imageRX));
+          meta.put(measureInfo + "imageRY", Integer.valueOf(imageRY));
+          meta.put(measureInfo + "xyGain", Short.valueOf(xyGain));
+          meta.put(measureInfo + "masterClock", Short.valueOf(masterClock));
+          meta.put(measureInfo + "adcDE", Short.valueOf(adcDE));
+          meta.put(measureInfo + "detType", Short.valueOf(detType));
+          meta.put(measureInfo + "xAxis", Short.valueOf(xAxis));
         }
       }
 
@@ -910,12 +910,12 @@ else if (token.indexOf(Y_IMG_STRING) != -1) {
         // save MeasHISTInfo to metadata table
         if (meta != null) {
           final String measHISTInfo = "MeasHISTInfo.";
-          meta.put(measHISTInfo + "fidaTime", new Float(fidaTime));
-          meta.put(measHISTInfo + "fildaTime", new Float(fildaTime));
-          meta.put(measHISTInfo + "fidaPoints", new Integer(fidaPoints));
-          meta.put(measHISTInfo + "fildaPoints", new Integer(fildaPoints));
-          meta.put(measHISTInfo + "mcsTime", new Float(mcsTime));
-          meta.put(measHISTInfo + "mcsPoints", new Integer(mcsPoints));
+          meta.put(measHISTInfo + "fidaTime", Float.valueOf(fidaTime));
+          meta.put(measHISTInfo + "fildaTime", Float.valueOf(fildaTime));
+          meta.put(measHISTInfo + "fidaPoints", Integer.valueOf(fidaPoints));
+          meta.put(measHISTInfo + "fildaPoints", Integer.valueOf(fildaPoints));
+          meta.put(measHISTInfo + "mcsTime", Float.valueOf(mcsTime));
+          meta.put(measHISTInfo + "mcsPoints", Integer.valueOf(mcsPoints));
         }
       }
     }
@@ -942,15 +942,15 @@ else if (token.indexOf(Y_IMG_STRING) != -1) {
       // save BHFileBlockHeader to metadata table
       if (meta != null) {
         final String bhFileBlockHeader = "BHFileBlockHeader.";
-        meta.put(bhFileBlockHeader + "blockNo", new Short(blockNo));
-        meta.put(bhFileBlockHeader + "dataOffs", new Integer(dataOffs));
+        meta.put(bhFileBlockHeader + "blockNo", Short.valueOf(blockNo));
+        meta.put(bhFileBlockHeader + "dataOffs", Integer.valueOf(dataOffs));
         meta.put(bhFileBlockHeader + "nextBlockOffs",
-          new Integer(nextBlockOffs));
-        meta.put(bhFileBlockHeader + "blockType", new Integer(blockType));
+          Integer.valueOf(nextBlockOffs));
+        meta.put(bhFileBlockHeader + "blockType", Integer.valueOf(blockType));
         meta.put(bhFileBlockHeader + "measDescBlockNo",
-          new Short(measDescBlockNo));
-        meta.put(bhFileBlockHeader + "lblockNo", new Long(lblockNo));
-        meta.put(bhFileBlockHeader + "blockLength", new Long(blockLength));
+          Short.valueOf(measDescBlockNo));
+        meta.put(bhFileBlockHeader + "lblockNo", Long.valueOf(lblockNo));
+        meta.put(bhFileBlockHeader + "blockLength", Long.valueOf(blockLength));
       }
 
       in.seek(nextBlockOffs);
diff --git a/components/formats-gpl/src/loci/formats/in/SVSReader.java b/components/formats-gpl/src/loci/formats/in/SVSReader.java
index b88b5478517..d3231b5bfdf 100644
--- a/components/formats-gpl/src/loci/formats/in/SVSReader.java
+++ b/components/formats-gpl/src/loci/formats/in/SVSReader.java
@@ -437,7 +437,7 @@ else if (macroIndex == -1) {
             key = t.substring(0, t.indexOf('=')).trim();
             value = t.substring(t.indexOf('=') + 1).trim();
             if (key.equals("TotalDepth")) {
-              zPosition[index] = new Double(0);
+              zPosition[index] = 0d;
             }
             else if (key.equals("OffsetZ")) {
               zPosition[index] = DataTools.parseDouble(value);
@@ -689,13 +689,13 @@ protected void initMetadataStore() throws FormatException {
 
       if (i == 0) {
         if (physicalDistanceFromTopEdge != null) {
-          Length yPos = FormatTools.getStagePosition(physicalDistanceFromTopEdge, UNITS.MM);
+          Length yPos = FormatTools.getStagePosition(physicalDistanceFromTopEdge, UNITS.MILLIMETER);
           for (int p=0; p<getImageCount(); p++) {
             store.setPlanePositionY(yPos, i, p);
           }
         }
         if (physicalDistanceFromLeftEdge != null) {
-          Length xPos = FormatTools.getStagePosition(physicalDistanceFromLeftEdge, UNITS.MM);
+          Length xPos = FormatTools.getStagePosition(physicalDistanceFromLeftEdge, UNITS.MILLIMETER);
           for (int p=0; p<getImageCount(); p++) {
             store.setPlanePositionX(xPos, i, p);
           }
diff --git a/components/formats-gpl/src/loci/formats/in/ScanrReader.java b/components/formats-gpl/src/loci/formats/in/ScanrReader.java
index 99cde8c5c40..64318040bc0 100644
--- a/components/formats-gpl/src/loci/formats/in/ScanrReader.java
+++ b/components/formats-gpl/src/loci/formats/in/ScanrReader.java
@@ -470,8 +470,8 @@ public int compare(String s1, String s2) {
         char row1 = s1.charAt(0);
         char row2 = s2.charAt(0);
 
-        final Integer col1 = new Integer(s1.substring(1));
-        final Integer col2 = new Integer(s2.substring(1));
+        final Integer col1 = Integer.parseInt(s1.substring(1));
+        final Integer col2 = Integer.parseInt(s2.substring(1));
 
         if (row1 < row2) {
           return -1;
@@ -830,7 +830,7 @@ else if (key.equals("plate name")) {
             plateName = v;
           }
           else if (key.equals("exposure time")) {
-            exposures.add(new Double(v));
+            exposures.add(DataTools.parseDouble(v));
           }
           else if (key.equals("idle") && validChannel) {
             int lastIndex = channelNames.size() - 1;
@@ -847,15 +847,15 @@ else if (key.equals("idle") && validChannel) {
           else if (key.equals("well selection table + cDNA")) {
             if (Character.isDigit(v.charAt(0))) {
               wellIndex = v;
-              wellNumbers.put(wellCount, new Integer(v));
+              wellNumbers.put(wellCount, Integer.parseInt(v));
               wellCount++;
             }
             else {
-              wellLabels.put(v, new Integer(wellIndex));
+              wellLabels.put(v, Integer.parseInt(wellIndex));
             }
           }
           else if (key.equals("conversion factor um/pixel")) {
-            pixelSize = new Double(v);
+            pixelSize = DataTools.parseDouble(v);
           }
           else if (foundPositions) {
             if (nextXPos == nextYPos) {
diff --git a/components/formats-gpl/src/loci/formats/in/SimplePCITiffReader.java b/components/formats-gpl/src/loci/formats/in/SimplePCITiffReader.java
index e4f451a0444..899a3043e0b 100644
--- a/components/formats-gpl/src/loci/formats/in/SimplePCITiffReader.java
+++ b/components/formats-gpl/src/loci/formats/in/SimplePCITiffReader.java
@@ -31,6 +31,7 @@
 import java.util.ArrayList;
 import java.util.HashMap;
 
+import loci.common.DataTools;
 import loci.common.DateTools;
 import loci.common.IniList;
 import loci.common.IniParser;
@@ -163,7 +164,7 @@ protected void initStandardMetadata() throws FormatException, IOException {
       String objective = microscopeTable.get("Objective");
       int space = objective.indexOf(' ');
       if (space != -1) {
-        magnification = new Double(objective.substring(0, space - 1));
+        magnification = DataTools.parseDouble(objective.substring(0, space - 1));
         immersion = objective.substring(space + 1);
       }
     }
@@ -192,7 +193,7 @@ protected void initStandardMetadata() throws FormatException, IOException {
       int index = 1;
       for (int i=0; i<getSizeC(); i++) {
         if (captureTable.get("c_Filter" + index) != null) {
-          exposureTimes.add(new Double(captureTable.get("c_Expos" + index)));
+          exposureTimes.add(DataTools.parseDouble(captureTable.get("c_Expos" + index)));
         }
         index++;
       }
diff --git a/components/formats-gpl/src/loci/formats/in/SlidebookTiffReader.java b/components/formats-gpl/src/loci/formats/in/SlidebookTiffReader.java
index 4010ec60dfd..3364627672d 100644
--- a/components/formats-gpl/src/loci/formats/in/SlidebookTiffReader.java
+++ b/components/formats-gpl/src/loci/formats/in/SlidebookTiffReader.java
@@ -29,6 +29,7 @@
 import java.util.ArrayList;
 import java.util.Arrays;
 
+import loci.common.DataTools;
 import loci.common.Location;
 import loci.common.RandomAccessInputStream;
 import loci.formats.CoreMetadata;
@@ -239,7 +240,7 @@ protected void initMetadataStore() throws FormatException {
       IFD ifd = ifds.get(0);
       String physicalSize = ifd.getIFDTextValue(PHYSICAL_SIZE_TAG);
       if (physicalSize != null) {
-        Double size = new Double(physicalSize);
+        Double size = DataTools.parseDouble(physicalSize);
         if (size > 0) {
           store.setPixelsPhysicalSizeX(FormatTools.getPhysicalSizeX(size), 0);
           store.setPixelsPhysicalSizeY(FormatTools.getPhysicalSizeY(size), 0);
@@ -252,7 +253,7 @@ protected void initMetadataStore() throws FormatException {
         store.setObjectiveID(MetadataTools.createLSID("Objective", 0, 0), 0, 0);
         store.setObjectiveCorrection(MetadataTools.getCorrection("Other"), 0, 0);
         store.setObjectiveImmersion(MetadataTools.getImmersion("Other"), 0, 0);
-        store.setObjectiveNominalMagnification(new Double(mag), 0, 0);
+        store.setObjectiveNominalMagnification(DataTools.parseDouble(mag), 0, 0);
       }
 
       final Double xn = Double.valueOf(ifd.getIFDTextValue(X_POS_TAG));
diff --git a/components/formats-gpl/src/loci/formats/in/SpiderReader.java b/components/formats-gpl/src/loci/formats/in/SpiderReader.java
index 1db9ed62015..f3e2d98e097 100644
--- a/components/formats-gpl/src/loci/formats/in/SpiderReader.java
+++ b/components/formats-gpl/src/loci/formats/in/SpiderReader.java
@@ -274,7 +274,7 @@ protected void initFile(String id) throws FormatException, IOException {
     }
 
     if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
-      Double size = new Double(pixelSize);
+      Double size = Double.valueOf(pixelSize);
       Length sizeX = FormatTools.getPhysicalSizeX(size, UNITS.ANGSTROM);
       Length sizeY = FormatTools.getPhysicalSizeY(size, UNITS.ANGSTROM);
       if (sizeX != null) {
diff --git a/components/formats-gpl/src/loci/formats/in/TCSReader.java b/components/formats-gpl/src/loci/formats/in/TCSReader.java
index 951a5fe05d2..e05296595f5 100644
--- a/components/formats-gpl/src/loci/formats/in/TCSReader.java
+++ b/components/formats-gpl/src/loci/formats/in/TCSReader.java
@@ -568,7 +568,7 @@ private void groupFiles() throws FormatException, IOException {
 
           String software = ifd.getIFDStringValue(IFD.SOFTWARE);
           if (software != null && software.trim().startsWith("TCS")) {
-            timestamps.put(file, new Long(stamp));
+            timestamps.put(file, Long.valueOf(stamp));
           }
         }
       }
diff --git a/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java b/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java
index c05d47da625..c84e5beb003 100644
--- a/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java
+++ b/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java
@@ -1424,7 +1424,7 @@ else if (extraIndex >= 0 && extraIndex < extraImages.size()) {
 
       if (airPressure != null) {
         store.setImagingEnvironmentAirPressure(
-                new Pressure(new Double(airPressure), UNITS.MILLIBAR), i);
+                new Pressure(DataTools.parseDouble(airPressure), UNITS.MILLIBAR), i);
       }
       if (co2Percent != null) {
         store.setImagingEnvironmentCO2Percent(
@@ -1436,21 +1436,21 @@ else if (extraIndex >= 0 && extraIndex < extraImages.size()) {
       }
       if (temperature != null) {
         store.setImagingEnvironmentTemperature(new Temperature(
-                new Double(temperature), UNITS.CELSIUS), i);
+                DataTools.parseDouble(temperature), UNITS.CELSIUS), i);
       }
 
       if (objectiveSettingsID != null) {
         store.setObjectiveSettingsID(objectiveSettingsID, i);
         if (correctionCollar != null) {
           store.setObjectiveSettingsCorrectionCollar(
-            new Double(correctionCollar), i);
+            DataTools.parseDouble(correctionCollar), i);
         }
         if (medium != null) {
           store.setObjectiveSettingsMedium(MetadataTools.getMedium(medium), i);
         }
         if (refractiveIndex != null) {
           store.setObjectiveSettingsRefractiveIndex(
-            new Double(refractiveIndex), i);
+            DataTools.parseDouble(refractiveIndex), i);
         }
       }
 
@@ -1687,7 +1687,7 @@ else if (getZCTCoords(plane)[2] < timestamps.size()) {
 
           String emWave = channels.get(c).emission;
           if (emWave != null) {
-            Double wave = new Double(emWave);
+            Double wave = DataTools.parseDouble(emWave);
             Length em = FormatTools.getEmissionWavelength(wave);
             if (em != null) {
               store.setChannelEmissionWavelength(em, i, c);
@@ -1695,7 +1695,7 @@ else if (getZCTCoords(plane)[2] < timestamps.size()) {
           }
           String exWave = channels.get(c).excitation;
           if (exWave != null) {
-            Double wave = new Double(exWave);
+            Double wave = DataTools.parseDouble(exWave);
             Length ex = FormatTools.getExcitationWavelength(wave);
             if (ex != null) {
               store.setChannelExcitationWavelength(ex, i, c);
@@ -1709,7 +1709,7 @@ else if (getZCTCoords(plane)[2] < timestamps.size()) {
 
           if (channels.get(c).pinhole != null) {
             store.setChannelPinholeSize(
-              new Length(new Double(channels.get(c).pinhole), UNITS.MICROMETER), i, c);
+              new Length(DataTools.parseDouble(channels.get(c).pinhole), UNITS.MICROMETER), i, c);
           }
 
           if (channels.get(c).acquisitionMode != null) {
@@ -2509,7 +2509,7 @@ private void translateInformation(Element root) throws FormatException {
           String power = getFirstNodeValue(lightSource, "Power");
           if ("Laser".equals(type)) {
             if (power != null) {
-              store.setLaserPower(new Power(new Double(power), UNITS.MILLIWATT), 0, i);
+              store.setLaserPower(new Power(DataTools.parseDouble(power), UNITS.MILLIWATT), 0, i);
             }
             store.setLaserLotNumber(lotNumber, 0, i);
             store.setLaserManufacturer(manufacturer, 0, i);
@@ -2518,7 +2518,7 @@ private void translateInformation(Element root) throws FormatException {
           }
           else if ("Arc".equals(type)) {
             if (power != null) {
-              store.setArcPower(new Power(new Double(power), UNITS.MILLIWATT), 0, i);
+              store.setArcPower(new Power(DataTools.parseDouble(power), UNITS.MILLIWATT), 0, i);
             }
             store.setArcLotNumber(lotNumber, 0, i);
             store.setArcManufacturer(manufacturer, 0, i);
@@ -2527,7 +2527,7 @@ else if ("Arc".equals(type)) {
           }
           else if ("LightEmittingDiode".equals(type)) {
             if (power != null) {
-              store.setLightEmittingDiodePower(new Power(new Double(power), UNITS.MILLIWATT), 0, i);
+              store.setLightEmittingDiodePower(new Power(DataTools.parseDouble(power), UNITS.MILLIWATT), 0, i);
             }
             store.setLightEmittingDiodeLotNumber(lotNumber, 0, i);
             store.setLightEmittingDiodeManufacturer(manufacturer, 0, i);
@@ -2536,7 +2536,7 @@ else if ("LightEmittingDiode".equals(type)) {
           }
           else if ("Filament".equals(type)) {
             if (power != null) {
-              store.setFilamentPower(new Power(new Double(power), UNITS.MILLIWATT), 0, i);
+              store.setFilamentPower(new Power(DataTools.parseDouble(power), UNITS.MILLIWATT), 0, i);
             }
             store.setFilamentLotNumber(lotNumber, 0, i);
             store.setFilamentManufacturer(manufacturer, 0, i);
@@ -2594,7 +2594,7 @@ else if ("Filament".equals(type)) {
 
           String offset = getFirstNodeValue(detector, "Offset");
           if (offset != null && !offset.equals("")) {
-            store.setDetectorOffset(new Double(offset), 0, detectorIndex);
+            store.setDetectorOffset(DataTools.parseDouble(offset), 0, detectorIndex);
           }
 
           zoom = getFirstNodeValue(detector, "Zoom");
@@ -2609,7 +2609,7 @@ else if ("Filament".equals(type)) {
 
           String ampGain = getFirstNodeValue(detector, "AmplificationGain");
           if (ampGain != null && !ampGain.equals("")) {
-            store.setDetectorAmplificationGain(new Double(ampGain), 0, detectorIndex);
+            store.setDetectorAmplificationGain(DataTools.parseDouble(ampGain), 0, detectorIndex);
           }
 
           String detectorType = getFirstNodeValue(detector, "Type");
@@ -2725,8 +2725,8 @@ else if ("Filament".equals(type)) {
 
           String cutIn = getFirstNodeValue(transmittance, "CutIn");
           String cutOut = getFirstNodeValue(transmittance, "CutOut");
-          Double inWave = cutIn == null ? 0 : new Double(cutIn);
-          Double outWave = cutOut == null ? 0 : new Double(cutOut);
+          Double inWave = cutIn == null ? 0 : DataTools.parseDouble(cutIn);
+          Double outWave = cutOut == null ? 0 : DataTools.parseDouble(cutOut);
 
           Length in = FormatTools.getCutIn(inWave);
           Length out = FormatTools.getCutOut(outWave);
@@ -2743,13 +2743,13 @@ else if ("Filament".equals(type)) {
             getFirstNodeValue(transmittance, "CutOutTolerance");
 
           if (inTolerance != null) {
-            Double cutInTolerance = new Double(inTolerance);
+            Double cutInTolerance = DataTools.parseDouble(inTolerance);
             store.setTransmittanceRangeCutInTolerance(
               new Length(cutInTolerance, UNITS.NANOMETER), 0, i);
           }
 
           if (outTolerance != null) {
-            Double cutOutTolerance = new Double(outTolerance);
+            Double cutOutTolerance = DataTools.parseDouble(outTolerance);
             store.setTransmittanceRangeCutOutTolerance(
               new Length(cutOutTolerance, UNITS.NANOMETER), 0, i);
           }
@@ -2813,7 +2813,13 @@ private void translateScaling(Element root) {
         if (originalValue == null) {
           continue;
         }
-        Double value = new Double(originalValue) * 1000000;
+        Double value = DataTools.parseDouble(originalValue);
+        if (value != null) {
+          value *= 1000000;
+        }
+        else {
+          value = 0d;
+        }
         if (value > 0) {
           PositiveFloat size = new PositiveFloat(value);
 
@@ -2940,20 +2946,23 @@ private void translateLayers(Element root) {
           String centerY = getFirstNodeValue(geometry, "CenterY");
 
           if (length != null) {
-            Double halfLen = new Double(length) / 2;
-            if (centerX != null) {
-              store.setLineX1(new Double(centerX) - halfLen, roiCount, shape);
-              store.setLineX2(new Double(centerX) + halfLen, roiCount, shape);
-
-              store.setLineX1(new Double(centerX), roiCount, shape + 1);
-              store.setLineX2(new Double(centerX), roiCount, shape + 1);
-            }
-            if (centerY != null) {
-              store.setLineY1(new Double(centerY), roiCount, shape);
-              store.setLineY2(new Double(centerY), roiCount, shape);
+            Double halfLen = DataTools.parseDouble(length);
+            if (halfLen != null) {
+              halfLen /= 2;
+              if (centerX != null) {
+                store.setLineX1(DataTools.parseDouble(centerX) - halfLen, roiCount, shape);
+                store.setLineX2(DataTools.parseDouble(centerX) + halfLen, roiCount, shape);
+
+                store.setLineX1(DataTools.parseDouble(centerX), roiCount, shape + 1);
+                store.setLineX2(DataTools.parseDouble(centerX), roiCount, shape + 1);
+              }
+              if (centerY != null) {
+                store.setLineY1(DataTools.parseDouble(centerY), roiCount, shape);
+                store.setLineY2(DataTools.parseDouble(centerY), roiCount, shape);
 
-              store.setLineY1(new Double(centerY) - halfLen, roiCount, shape + 1);
-              store.setLineY2(new Double(centerY) + halfLen, roiCount, shape + 1);
+                store.setLineY1(DataTools.parseDouble(centerY) - halfLen, roiCount, shape + 1);
+                store.setLineY2(DataTools.parseDouble(centerY) + halfLen, roiCount, shape + 1);
+              }
             }
           }
           store.setLineText(getFirstNodeValue(textElements, "Text"), roiCount, shape);
@@ -2983,16 +2992,16 @@ private void translateLayers(Element root) {
             String centerY = getFirstNodeValue(geometry, "CenterY");
 
             if (radiusX != null) {
-              store.setEllipseRadiusX(new Double(radiusX), roiCount, shape);
+              store.setEllipseRadiusX(DataTools.parseDouble(radiusX), roiCount, shape);
             }
             if (radiusY != null) {
-              store.setEllipseRadiusY(new Double(radiusY), roiCount, shape);
+              store.setEllipseRadiusY(DataTools.parseDouble(radiusY), roiCount, shape);
             }
             if (centerX != null) {
-              store.setEllipseX(new Double(centerX), roiCount, shape);
+              store.setEllipseX(DataTools.parseDouble(centerX), roiCount, shape);
             }
             if (centerY != null) {
-              store.setEllipseY(new Double(centerY), roiCount, shape);
+              store.setEllipseY(DataTools.parseDouble(centerY), roiCount, shape);
             }
             store.setEllipseText(
               getFirstNodeValue(textElements, "Text"), roiCount, shape);
@@ -3165,7 +3174,7 @@ private void translateHardwareSettings(Element root) throws FormatException {
           if (magnification != null) {
             try {
               store.setObjectiveNominalMagnification(
-                new Double(magnification), 0, i);
+                DataTools.parseDouble(magnification), 0, i);
             }
             catch (NumberFormatException e) {
               LOGGER.debug("Could not parse magnification", e);
@@ -3173,7 +3182,7 @@ private void translateHardwareSettings(Element root) throws FormatException {
           }
           if (na != null) {
             try {
-              store.setObjectiveLensNA(new Double(na), 0, i);
+              store.setObjectiveLensNA(DataTools.parseDouble(na), 0, i);
             }
             catch (NumberFormatException e) {
               LOGGER.debug("Could not parse numerical aperture", e);
@@ -3181,7 +3190,7 @@ private void translateHardwareSettings(Element root) throws FormatException {
           }
           if (wd != null) {
             try {
-              store.setObjectiveWorkingDistance(new Length(new Double(wd), UNITS.MICROMETER), 0, i);
+              store.setObjectiveWorkingDistance(new Length(DataTools.parseDouble(wd), UNITS.MICROMETER), 0, i);
             }
             catch (NumberFormatException e) {
               LOGGER.debug("Could not parse working distance", e);
@@ -3209,10 +3218,10 @@ private int populateRectangles(NodeList rectangles, int roi, int shape) {
       if (left != null && top != null && width != null && height != null) {
         store.setRectangleID(
           MetadataTools.createLSID("Shape", roi, shape), roi, shape);
-        store.setRectangleX(new Double(left), roi, shape);
-        store.setRectangleY(new Double(top), roi, shape);
-        store.setRectangleWidth(new Double(width), roi, shape);
-        store.setRectangleHeight(new Double(height), roi, shape);
+        store.setRectangleX(DataTools.parseDouble(left), roi, shape);
+        store.setRectangleY(DataTools.parseDouble(top), roi, shape);
+        store.setRectangleWidth(DataTools.parseDouble(width), roi, shape);
+        store.setRectangleHeight(DataTools.parseDouble(height), roi, shape);
 
         String name = getFirstNodeValue(attributes, "Name");
         String label = getFirstNodeValue(textElements, "Text");
@@ -3272,16 +3281,16 @@ private int populateLines(NodeList lines, int roi, int shape) {
         MetadataTools.createLSID("Shape", roi, shape), roi, shape);
 
       if (x1 != null) {
-        store.setLineX1(new Double(x1), roi, shape);
+        store.setLineX1(DataTools.parseDouble(x1), roi, shape);
       }
       if (x2 != null) {
-        store.setLineX2(new Double(x2), roi, shape);
+        store.setLineX2(DataTools.parseDouble(x2), roi, shape);
       }
       if (y1 != null) {
-        store.setLineY1(new Double(y1), roi, shape);
+        store.setLineY1(DataTools.parseDouble(y1), roi, shape);
       }
       if (y2 != null) {
-        store.setLineY2(new Double(y2), roi, shape);
+        store.setLineY2(DataTools.parseDouble(y2), roi, shape);
       }
       store.setLineText(getFirstNodeValue(textElements, "Text"), roi, shape);
     }
@@ -3302,14 +3311,14 @@ private int populateCircles(NodeList circles, int roi, int shape) {
       String centerY = getFirstNodeValue(geometry, "CenterY");
 
       if (radius != null) {
-        store.setEllipseRadiusX(new Double(radius), roi, shape);
-        store.setEllipseRadiusY(new Double(radius), roi, shape);
+        store.setEllipseRadiusX(DataTools.parseDouble(radius), roi, shape);
+        store.setEllipseRadiusY(DataTools.parseDouble(radius), roi, shape);
       }
       if (centerX != null) {
-        store.setEllipseX(new Double(centerX), roi, shape);
+        store.setEllipseX(DataTools.parseDouble(centerX), roi, shape);
       }
       if (centerY != null) {
-        store.setEllipseY(new Double(centerY), roi, shape);
+        store.setEllipseY(DataTools.parseDouble(centerY), roi, shape);
       }
       store.setEllipseText(getFirstNodeValue(textElements, "Text"), roi, shape);
     }
@@ -3535,7 +3544,7 @@ private void translateExperiment(Element root) throws FormatException {
 
         try {
           if (exposure != null) {
-            channels.get(i).exposure = new Double(exposure);
+            channels.get(i).exposure = DataTools.parseDouble(exposure);
           }
         }
         catch (NumberFormatException e) {
@@ -3543,7 +3552,7 @@ private void translateExperiment(Element root) throws FormatException {
         }
         try {
           if (gain != null) {
-            channels.get(i).gain = new Double(gain);
+            channels.get(i).gain = DataTools.parseDouble(gain);
           }
         }
         catch (NumberFormatException e) {
@@ -3825,7 +3834,7 @@ private void parseObjectives(NodeList objectives) throws FormatException {
 
         String lensNA = getFirstNodeValue(objective, "LensNA");
         if (lensNA != null) {
-          store.setObjectiveLensNA(new Double(lensNA), 0, i);
+          store.setObjectiveLensNA(DataTools.parseDouble(lensNA), 0, i);
         }
 
         String magnification =
@@ -3833,7 +3842,7 @@ private void parseObjectives(NodeList objectives) throws FormatException {
         if (magnification == null) {
           magnification = getFirstNodeValue(objective, "Magnification");
         }
-        Double mag = magnification == null ? null : new Double(magnification);
+        Double mag = magnification == null ? null : DataTools.parseDouble(magnification);
 
         if (mag != null) {
           store.setObjectiveNominalMagnification(mag, 0, i);
@@ -3842,15 +3851,15 @@ private void parseObjectives(NodeList objectives) throws FormatException {
           getFirstNodeValue(objective, "CalibratedMagnification");
         if (calibratedMag != null) {
           store.setObjectiveCalibratedMagnification(
-            new Double(calibratedMag), 0, i);
+            DataTools.parseDouble(calibratedMag), 0, i);
         }
         String wd = getFirstNodeValue(objective, "WorkingDistance");
         if (wd != null) {
-          store.setObjectiveWorkingDistance(new Length(new Double(wd), UNITS.MICROMETER), 0, i);
+          store.setObjectiveWorkingDistance(new Length(DataTools.parseDouble(wd), UNITS.MICROMETER), 0, i);
         }
         String iris = getFirstNodeValue(objective, "Iris");
         if (iris != null) {
-          store.setObjectiveIris(new Boolean(iris), 0, i);
+          store.setObjectiveIris(Boolean.parseBoolean(iris), 0, i);
         }
       }
     }
@@ -4286,7 +4295,7 @@ else if (tagNode.getNodeName().equals("AcquisitionTime")) {
                     timestamp = t.asInstant().getMillis() / 1000d;
                 }
                 else if (tagNode.getNodeName().equals("ExposureTime")) {
-                  exposureTime = new Double(text);
+                  exposureTime = DataTools.parseDouble(text);
                 }
               }
             }
diff --git a/components/formats-gpl/src/loci/formats/in/ZeissLSMReader.java b/components/formats-gpl/src/loci/formats/in/ZeissLSMReader.java
index ed22ac83ba9..cf7e82bdce1 100644
--- a/components/formats-gpl/src/loci/formats/in/ZeissLSMReader.java
+++ b/components/formats-gpl/src/loci/formats/in/ZeissLSMReader.java
@@ -1486,7 +1486,7 @@ nextDetectChannel < getSizeC() && channel.acquire)
           String transmittance = channel.filter.substring(space + 1).trim();
           String[] v = transmittance.split("-");
           try {
-            final Double cutIn = new Double(v[0].trim());
+            final Double cutIn = DataTools.parseDouble(v[0].trim());
             Length in = FormatTools.getCutIn(cutIn);
             if (in != null) {
               store.setTransmittanceRangeCutIn(in, instrument, nextFilter);
@@ -1495,7 +1495,7 @@ nextDetectChannel < getSizeC() && channel.acquire)
           catch (NumberFormatException e) { }
           if (v.length > 1) {
             try {
-              final Double cutOut = new Double(v[1].trim());
+              final Double cutOut = DataTools.parseDouble(v[1].trim());
               Length out = FormatTools.getCutOut(cutOut);
               if (out != null) {
                 store.setTransmittanceRangeCutOut(out, instrument, nextFilter);
@@ -2410,13 +2410,13 @@ protected void read() throws IOException {
         int slash = p.indexOf('/');
         if (slash > 0) {
           try {
-            magnification = new Double(p.substring(0, slash - 1));
+            magnification = DataTools.parseDouble(p.substring(0, slash - 1));
           }
           catch (NumberFormatException e) { }
         }
         if (slash >= 0 && slash < p.length() - 1) {
           try {
-            lensNA = new Double(p.substring(slash + 1));
+            lensNA = DataTools.parseDouble(p.substring(slash + 1));
           }
           catch (NumberFormatException e) { }
         }
@@ -2519,7 +2519,7 @@ protected void read() throws IOException {
 
       name = getStringValue(ILLUM_CHANNEL_NAME);
       try {
-        wavelength = new Double(name);
+        wavelength = DataTools.parseDouble(name);
       }
       catch (NumberFormatException e) { }
     }

From 7865d78773015abbea3a5fd5c04eeec021949dd8 Mon Sep 17 00:00:00 2001
From: Melissa Linkert <melissa@glencoesoftware.com>
Date: Mon, 22 Apr 2024 15:51:50 -0500
Subject: [PATCH 2/3] Use Double.parseDouble instead of DataTools.parseDouble
 to fix test failures

---
 .../src/loci/formats/in/BaseZeissReader.java  |  21 ++-
 .../src/loci/formats/in/CellWorxReader.java   |  14 +-
 .../src/loci/formats/in/ND2Handler.java       |  11 +-
 .../src/loci/formats/in/ZeissCZIReader.java   | 123 ++++++++----------
 4 files changed, 77 insertions(+), 92 deletions(-)

diff --git a/components/formats-gpl/src/loci/formats/in/BaseZeissReader.java b/components/formats-gpl/src/loci/formats/in/BaseZeissReader.java
index 4e116091e1b..6327b32f2e6 100644
--- a/components/formats-gpl/src/loci/formats/in/BaseZeissReader.java
+++ b/components/formats-gpl/src/loci/formats/in/BaseZeissReader.java
@@ -36,7 +36,6 @@
 import java.util.ArrayList;
 import java.lang.Math;
 
-import loci.common.DataTools;
 import loci.common.DateTools;
 import loci.formats.CoreMetadata;
 import loci.formats.FormatTools;
@@ -401,12 +400,10 @@ protected void fillMetadataPass7(MetadataStore store) throws FormatException, IO
             exposure = exposureTime.values().iterator().next();
           }
           Double exp = 0d;
-          try { exp = DataTools.parseDouble(exposure); }
+          try { exp = Double.parseDouble(exposure); }
           catch (NumberFormatException e) { }
           catch (NullPointerException e) { }
-          if (exp != null) {
-            store.setPlaneExposureTime(new Time(exp, UNITS.SECOND), i, plane);
-          }
+          store.setPlaneExposureTime(new Time(exp, UNITS.SECOND), i, plane);
 
           int posIndex = i * getImageCount() + plane;
 
@@ -913,7 +910,7 @@ else if (key.startsWith("NumberOfRawImages") && rawCount == 0)
         }
         else if (key.startsWith("Emission Wavelength")) {
           if (cIndex != -1) {
-            Double wave = DataTools.parseDouble(value);
+            Double wave = Double.parseDouble(value);
             Length emission = FormatTools.getEmissionWavelength(wave);
             if (emission != null) {
               emWavelength.put(cIndex, emission);
@@ -922,7 +919,7 @@ else if (key.startsWith("Emission Wavelength")) {
         }
         else if (key.startsWith("Excitation Wavelength")) {
           if (cIndex != -1) {
-            Double wave = DataTools.parseDouble(value);
+            Double wave = Double.parseDouble(value);
             Length excitation = FormatTools.getExcitationWavelength(wave);
             if (excitation != null) {
               exWavelength.put(cIndex, excitation);
@@ -964,7 +961,7 @@ else if (key.startsWith("Objective ID")) {
           store.setObjectiveImmersion(MetadataTools.getImmersion("Other"), 0, 0);
         }
         else if (key.startsWith("Objective N.A.")) {
-          store.setObjectiveLensNA(DataTools.parseDouble(value), 0, 0);
+          store.setObjectiveLensNA(Double.parseDouble(value), 0, 0);
         }
         else if (key.startsWith("Objective Name")) {
           String[] tokens = value.split(" ");
@@ -975,14 +972,14 @@ else if (key.startsWith("Objective Name")) {
                   Double.parseDouble(tokens[q].substring(0, slash - q));
               String na = tokens[q].substring(slash + 1);
               store.setObjectiveNominalMagnification(mag, 0, 0);
-              store.setObjectiveLensNA(DataTools.parseDouble(na), 0, 0);
+              store.setObjectiveLensNA(Double.parseDouble(na), 0, 0);
               store.setObjectiveCorrection(MetadataTools.getCorrection(tokens[q - 1]), 0, 0);
               break;
             }
           }
         }
         else if (key.startsWith("Objective Working Distance")) {
-          store.setObjectiveWorkingDistance(new Length(DataTools.parseDouble(value), UNITS.MICROMETER), 0, 0);
+          store.setObjectiveWorkingDistance(new Length(Double.parseDouble(value), UNITS.MICROMETER), 0, 0);
         }
         else if (key.startsWith("Objective Immersion Type")) {
           String immersion = "Other";
@@ -1008,10 +1005,10 @@ else if (key.startsWith("Stage Position Y")) {
           addGlobalMetaList("Y position for position", value);
         }
         else if (key.startsWith("Orca Analog Gain")) {
-          detectorGain.put(cIndex, DataTools.parseDouble(value));
+          detectorGain.put(cIndex, Double.parseDouble(value));
         }
         else if (key.startsWith("Orca Analog Offset")) {
-          detectorOffset.put(cIndex, DataTools.parseDouble(value));
+          detectorOffset.put(cIndex, Double.parseDouble(value));
         }
         else if (key.startsWith("Comments")) {
           imageDescription = value;
diff --git a/components/formats-gpl/src/loci/formats/in/CellWorxReader.java b/components/formats-gpl/src/loci/formats/in/CellWorxReader.java
index 1cd3593464d..4b603927a4d 100644
--- a/components/formats-gpl/src/loci/formats/in/CellWorxReader.java
+++ b/components/formats-gpl/src/loci/formats/in/CellWorxReader.java
@@ -778,8 +778,8 @@ protected void parseWellLogFile(int wellIndex, MetadataStore store)
       }
       else if (key.equals("Scan Origin")) {
         String[] axes = value.split(",");
-        Double posX = DataTools.parseDouble(axes[0]);
-        Double posY = DataTools.parseDouble(axes[1]);
+        Double posX = Double.parseDouble(axes[0]);
+        Double posY = Double.parseDouble(axes[1]);
         for (int fieldRow=0; fieldRow<fieldMap.length; fieldRow++) {
           for (int fieldCol=0; fieldCol<fieldMap[fieldRow].length; fieldCol++) {
             if (fieldMap[fieldRow][fieldCol] && wellFiles[row][col] != null) {
@@ -799,8 +799,8 @@ else if (key.equals("Scan Area")) {
         int s = value.indexOf('x');
         if (s > 0) {
           int end = value.indexOf(" ", s + 2);
-          Double xSize = DataTools.parseDouble(value.substring(0, s).trim());
-          Double ySize = DataTools.parseDouble(value.substring(s + 1, end).trim());
+          Double xSize = Double.parseDouble(value.substring(0, s).trim());
+          Double ySize = Double.parseDouble(value.substring(s + 1, end).trim());
 
           Length x = FormatTools.getPhysicalSizeX(xSize / getSizeX());
           Length y = FormatTools.getPhysicalSizeY(ySize / getSizeY());
@@ -827,7 +827,7 @@ else if (key.startsWith("Channel")) {
           token = token.trim();
           if (token.startsWith("gain")) {
             String instrumentID = MetadataTools.createLSID("Instrument", 0);
-            Double gain = DataTools.parseDouble(token.replaceAll("gain ", ""));
+            Double gain = Double.parseDouble(token.replaceAll("gain ", ""));
             String detectorID = MetadataTools.createLSID("Detector", 0, 0);
 
             store.setInstrumentID(instrumentID, 0);
@@ -854,8 +854,8 @@ else if (token.startsWith("EX")) {
                 }
               }
 
-              Double emission = DataTools.parseDouble(em);
-              Double excitation = DataTools.parseDouble(ex);
+              Double emission = Double.parseDouble(em);
+              Double excitation = Double.parseDouble(ex);
 
               Length exWave = FormatTools.getExcitationWavelength(excitation);
               Length emWave = FormatTools.getEmissionWavelength(emission);
diff --git a/components/formats-gpl/src/loci/formats/in/ND2Handler.java b/components/formats-gpl/src/loci/formats/in/ND2Handler.java
index 7a4dc80740f..48d11f30895 100644
--- a/components/formats-gpl/src/loci/formats/in/ND2Handler.java
+++ b/components/formats-gpl/src/loci/formats/in/ND2Handler.java
@@ -154,7 +154,7 @@ public void populateROIs(MetadataStore store) {
           store.setLabelFontSize(new Length(fontSize, UNITS.POINT), r, 0);
         }
         store.setLabelText(roi.get("eval-text"), r, 0);
-        Length l = new Length(DataTools.parseDouble(roi.get("line-width")), UNITS.PIXEL);
+        Length l = new Length(Double.parseDouble(roi.get("line-width")), UNITS.PIXEL);
         store.setLabelStrokeWidth(l, r, 0);
 
         String rectangle = roi.get("rectangle");
@@ -885,11 +885,11 @@ else if (key.equals("Line")) {
       }
       else if (key.equalsIgnoreCase("Emission wavelength")) {
         String[] v = value.split(" ");
-        emWave.add(DataTools.parseDouble(v[0]));
+        emWave.add(Double.parseDouble(v[0]));
       }
       else if (key.equalsIgnoreCase("Excitation wavelength")) {
         String[] v = value.split(" ");
-        exWave.add(DataTools.parseDouble(v[0]));
+        exWave.add(Double.parseDouble(v[0]));
       }
       else if (key.equals("Power")) {
         power.add(DataTools.parseDouble(value).intValue());
@@ -898,10 +898,7 @@ else if (key.equals("CameraUniqueName")) {
         cameraModel = value;
       }
       else if (key.equals("ExposureTime")) {
-        Double time = DataTools.parseDouble(value);
-        if (time != null) {
-          exposureTime.add(time / 1000d);
-        }
+        exposureTime.add(Double.parseDouble(value) / 1000d);
       }
       else if (key.equals("sDate")) {
         date = DateTools.formatDate(value, DATE_FORMAT);
diff --git a/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java b/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java
index c84e5beb003..db5d505a895 100644
--- a/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java
+++ b/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java
@@ -1424,7 +1424,7 @@ else if (extraIndex >= 0 && extraIndex < extraImages.size()) {
 
       if (airPressure != null) {
         store.setImagingEnvironmentAirPressure(
-                new Pressure(DataTools.parseDouble(airPressure), UNITS.MILLIBAR), i);
+                new Pressure(Double.parseDouble(airPressure), UNITS.MILLIBAR), i);
       }
       if (co2Percent != null) {
         store.setImagingEnvironmentCO2Percent(
@@ -1436,21 +1436,21 @@ else if (extraIndex >= 0 && extraIndex < extraImages.size()) {
       }
       if (temperature != null) {
         store.setImagingEnvironmentTemperature(new Temperature(
-                DataTools.parseDouble(temperature), UNITS.CELSIUS), i);
+                Double.parseDouble(temperature), UNITS.CELSIUS), i);
       }
 
       if (objectiveSettingsID != null) {
         store.setObjectiveSettingsID(objectiveSettingsID, i);
         if (correctionCollar != null) {
           store.setObjectiveSettingsCorrectionCollar(
-            DataTools.parseDouble(correctionCollar), i);
+            Double.parseDouble(correctionCollar), i);
         }
         if (medium != null) {
           store.setObjectiveSettingsMedium(MetadataTools.getMedium(medium), i);
         }
         if (refractiveIndex != null) {
           store.setObjectiveSettingsRefractiveIndex(
-            DataTools.parseDouble(refractiveIndex), i);
+            Double.parseDouble(refractiveIndex), i);
         }
       }
 
@@ -1687,7 +1687,7 @@ else if (getZCTCoords(plane)[2] < timestamps.size()) {
 
           String emWave = channels.get(c).emission;
           if (emWave != null) {
-            Double wave = DataTools.parseDouble(emWave);
+            Double wave = Double.parseDouble(emWave);
             Length em = FormatTools.getEmissionWavelength(wave);
             if (em != null) {
               store.setChannelEmissionWavelength(em, i, c);
@@ -1695,7 +1695,7 @@ else if (getZCTCoords(plane)[2] < timestamps.size()) {
           }
           String exWave = channels.get(c).excitation;
           if (exWave != null) {
-            Double wave = DataTools.parseDouble(exWave);
+            Double wave = Double.parseDouble(exWave);
             Length ex = FormatTools.getExcitationWavelength(wave);
             if (ex != null) {
               store.setChannelExcitationWavelength(ex, i, c);
@@ -1709,7 +1709,7 @@ else if (getZCTCoords(plane)[2] < timestamps.size()) {
 
           if (channels.get(c).pinhole != null) {
             store.setChannelPinholeSize(
-              new Length(DataTools.parseDouble(channels.get(c).pinhole), UNITS.MICROMETER), i, c);
+              new Length(Double.parseDouble(channels.get(c).pinhole), UNITS.MICROMETER), i, c);
           }
 
           if (channels.get(c).acquisitionMode != null) {
@@ -2509,7 +2509,7 @@ private void translateInformation(Element root) throws FormatException {
           String power = getFirstNodeValue(lightSource, "Power");
           if ("Laser".equals(type)) {
             if (power != null) {
-              store.setLaserPower(new Power(DataTools.parseDouble(power), UNITS.MILLIWATT), 0, i);
+              store.setLaserPower(new Power(Double.parseDouble(power), UNITS.MILLIWATT), 0, i);
             }
             store.setLaserLotNumber(lotNumber, 0, i);
             store.setLaserManufacturer(manufacturer, 0, i);
@@ -2518,7 +2518,7 @@ private void translateInformation(Element root) throws FormatException {
           }
           else if ("Arc".equals(type)) {
             if (power != null) {
-              store.setArcPower(new Power(DataTools.parseDouble(power), UNITS.MILLIWATT), 0, i);
+              store.setArcPower(new Power(Double.parseDouble(power), UNITS.MILLIWATT), 0, i);
             }
             store.setArcLotNumber(lotNumber, 0, i);
             store.setArcManufacturer(manufacturer, 0, i);
@@ -2527,7 +2527,7 @@ else if ("Arc".equals(type)) {
           }
           else if ("LightEmittingDiode".equals(type)) {
             if (power != null) {
-              store.setLightEmittingDiodePower(new Power(DataTools.parseDouble(power), UNITS.MILLIWATT), 0, i);
+              store.setLightEmittingDiodePower(new Power(Double.parseDouble(power), UNITS.MILLIWATT), 0, i);
             }
             store.setLightEmittingDiodeLotNumber(lotNumber, 0, i);
             store.setLightEmittingDiodeManufacturer(manufacturer, 0, i);
@@ -2536,7 +2536,7 @@ else if ("LightEmittingDiode".equals(type)) {
           }
           else if ("Filament".equals(type)) {
             if (power != null) {
-              store.setFilamentPower(new Power(DataTools.parseDouble(power), UNITS.MILLIWATT), 0, i);
+              store.setFilamentPower(new Power(Double.parseDouble(power), UNITS.MILLIWATT), 0, i);
             }
             store.setFilamentLotNumber(lotNumber, 0, i);
             store.setFilamentManufacturer(manufacturer, 0, i);
@@ -2594,7 +2594,7 @@ else if ("Filament".equals(type)) {
 
           String offset = getFirstNodeValue(detector, "Offset");
           if (offset != null && !offset.equals("")) {
-            store.setDetectorOffset(DataTools.parseDouble(offset), 0, detectorIndex);
+            store.setDetectorOffset(Double.parseDouble(offset), 0, detectorIndex);
           }
 
           zoom = getFirstNodeValue(detector, "Zoom");
@@ -2609,7 +2609,7 @@ else if ("Filament".equals(type)) {
 
           String ampGain = getFirstNodeValue(detector, "AmplificationGain");
           if (ampGain != null && !ampGain.equals("")) {
-            store.setDetectorAmplificationGain(DataTools.parseDouble(ampGain), 0, detectorIndex);
+            store.setDetectorAmplificationGain(Double.parseDouble(ampGain), 0, detectorIndex);
           }
 
           String detectorType = getFirstNodeValue(detector, "Type");
@@ -2725,8 +2725,8 @@ else if ("Filament".equals(type)) {
 
           String cutIn = getFirstNodeValue(transmittance, "CutIn");
           String cutOut = getFirstNodeValue(transmittance, "CutOut");
-          Double inWave = cutIn == null ? 0 : DataTools.parseDouble(cutIn);
-          Double outWave = cutOut == null ? 0 : DataTools.parseDouble(cutOut);
+          Double inWave = cutIn == null ? 0 : Double.parseDouble(cutIn);
+          Double outWave = cutOut == null ? 0 : Double.parseDouble(cutOut);
 
           Length in = FormatTools.getCutIn(inWave);
           Length out = FormatTools.getCutOut(outWave);
@@ -2743,13 +2743,13 @@ else if ("Filament".equals(type)) {
             getFirstNodeValue(transmittance, "CutOutTolerance");
 
           if (inTolerance != null) {
-            Double cutInTolerance = DataTools.parseDouble(inTolerance);
+            Double cutInTolerance = Double.parseDouble(inTolerance);
             store.setTransmittanceRangeCutInTolerance(
               new Length(cutInTolerance, UNITS.NANOMETER), 0, i);
           }
 
           if (outTolerance != null) {
-            Double cutOutTolerance = DataTools.parseDouble(outTolerance);
+            Double cutOutTolerance = Double.parseDouble(outTolerance);
             store.setTransmittanceRangeCutOutTolerance(
               new Length(cutOutTolerance, UNITS.NANOMETER), 0, i);
           }
@@ -2813,13 +2813,7 @@ private void translateScaling(Element root) {
         if (originalValue == null) {
           continue;
         }
-        Double value = DataTools.parseDouble(originalValue);
-        if (value != null) {
-          value *= 1000000;
-        }
-        else {
-          value = 0d;
-        }
+        Double value = Double.parseDouble(originalValue) * 1000000;
         if (value > 0) {
           PositiveFloat size = new PositiveFloat(value);
 
@@ -2946,23 +2940,20 @@ private void translateLayers(Element root) {
           String centerY = getFirstNodeValue(geometry, "CenterY");
 
           if (length != null) {
-            Double halfLen = DataTools.parseDouble(length);
-            if (halfLen != null) {
-              halfLen /= 2;
-              if (centerX != null) {
-                store.setLineX1(DataTools.parseDouble(centerX) - halfLen, roiCount, shape);
-                store.setLineX2(DataTools.parseDouble(centerX) + halfLen, roiCount, shape);
-
-                store.setLineX1(DataTools.parseDouble(centerX), roiCount, shape + 1);
-                store.setLineX2(DataTools.parseDouble(centerX), roiCount, shape + 1);
-              }
-              if (centerY != null) {
-                store.setLineY1(DataTools.parseDouble(centerY), roiCount, shape);
-                store.setLineY2(DataTools.parseDouble(centerY), roiCount, shape);
+            Double halfLen = Double.parseDouble(length) / 2;
+            if (centerX != null) {
+              store.setLineX1(Double.parseDouble(centerX) - halfLen, roiCount, shape);
+              store.setLineX2(Double.parseDouble(centerX) + halfLen, roiCount, shape);
 
-                store.setLineY1(DataTools.parseDouble(centerY) - halfLen, roiCount, shape + 1);
-                store.setLineY2(DataTools.parseDouble(centerY) + halfLen, roiCount, shape + 1);
-              }
+              store.setLineX1(Double.parseDouble(centerX), roiCount, shape + 1);
+              store.setLineX2(Double.parseDouble(centerX), roiCount, shape + 1);
+            }
+            if (centerY != null) {
+              store.setLineY1(Double.parseDouble(centerY), roiCount, shape);
+              store.setLineY2(Double.parseDouble(centerY), roiCount, shape);
+
+              store.setLineY1(Double.parseDouble(centerY) - halfLen, roiCount, shape + 1);
+              store.setLineY2(Double.parseDouble(centerY) + halfLen, roiCount, shape + 1);
             }
           }
           store.setLineText(getFirstNodeValue(textElements, "Text"), roiCount, shape);
@@ -2992,16 +2983,16 @@ private void translateLayers(Element root) {
             String centerY = getFirstNodeValue(geometry, "CenterY");
 
             if (radiusX != null) {
-              store.setEllipseRadiusX(DataTools.parseDouble(radiusX), roiCount, shape);
+              store.setEllipseRadiusX(Double.parseDouble(radiusX), roiCount, shape);
             }
             if (radiusY != null) {
-              store.setEllipseRadiusY(DataTools.parseDouble(radiusY), roiCount, shape);
+              store.setEllipseRadiusY(Double.parseDouble(radiusY), roiCount, shape);
             }
             if (centerX != null) {
-              store.setEllipseX(DataTools.parseDouble(centerX), roiCount, shape);
+              store.setEllipseX(Double.parseDouble(centerX), roiCount, shape);
             }
             if (centerY != null) {
-              store.setEllipseY(DataTools.parseDouble(centerY), roiCount, shape);
+              store.setEllipseY(Double.parseDouble(centerY), roiCount, shape);
             }
             store.setEllipseText(
               getFirstNodeValue(textElements, "Text"), roiCount, shape);
@@ -3174,7 +3165,7 @@ private void translateHardwareSettings(Element root) throws FormatException {
           if (magnification != null) {
             try {
               store.setObjectiveNominalMagnification(
-                DataTools.parseDouble(magnification), 0, i);
+                Double.parseDouble(magnification), 0, i);
             }
             catch (NumberFormatException e) {
               LOGGER.debug("Could not parse magnification", e);
@@ -3182,7 +3173,7 @@ private void translateHardwareSettings(Element root) throws FormatException {
           }
           if (na != null) {
             try {
-              store.setObjectiveLensNA(DataTools.parseDouble(na), 0, i);
+              store.setObjectiveLensNA(Double.parseDouble(na), 0, i);
             }
             catch (NumberFormatException e) {
               LOGGER.debug("Could not parse numerical aperture", e);
@@ -3190,7 +3181,7 @@ private void translateHardwareSettings(Element root) throws FormatException {
           }
           if (wd != null) {
             try {
-              store.setObjectiveWorkingDistance(new Length(DataTools.parseDouble(wd), UNITS.MICROMETER), 0, i);
+              store.setObjectiveWorkingDistance(new Length(Double.parseDouble(wd), UNITS.MICROMETER), 0, i);
             }
             catch (NumberFormatException e) {
               LOGGER.debug("Could not parse working distance", e);
@@ -3218,10 +3209,10 @@ private int populateRectangles(NodeList rectangles, int roi, int shape) {
       if (left != null && top != null && width != null && height != null) {
         store.setRectangleID(
           MetadataTools.createLSID("Shape", roi, shape), roi, shape);
-        store.setRectangleX(DataTools.parseDouble(left), roi, shape);
-        store.setRectangleY(DataTools.parseDouble(top), roi, shape);
-        store.setRectangleWidth(DataTools.parseDouble(width), roi, shape);
-        store.setRectangleHeight(DataTools.parseDouble(height), roi, shape);
+        store.setRectangleX(Double.parseDouble(left), roi, shape);
+        store.setRectangleY(Double.parseDouble(top), roi, shape);
+        store.setRectangleWidth(Double.parseDouble(width), roi, shape);
+        store.setRectangleHeight(Double.parseDouble(height), roi, shape);
 
         String name = getFirstNodeValue(attributes, "Name");
         String label = getFirstNodeValue(textElements, "Text");
@@ -3281,16 +3272,16 @@ private int populateLines(NodeList lines, int roi, int shape) {
         MetadataTools.createLSID("Shape", roi, shape), roi, shape);
 
       if (x1 != null) {
-        store.setLineX1(DataTools.parseDouble(x1), roi, shape);
+        store.setLineX1(Double.parseDouble(x1), roi, shape);
       }
       if (x2 != null) {
-        store.setLineX2(DataTools.parseDouble(x2), roi, shape);
+        store.setLineX2(Double.parseDouble(x2), roi, shape);
       }
       if (y1 != null) {
-        store.setLineY1(DataTools.parseDouble(y1), roi, shape);
+        store.setLineY1(Double.parseDouble(y1), roi, shape);
       }
       if (y2 != null) {
-        store.setLineY2(DataTools.parseDouble(y2), roi, shape);
+        store.setLineY2(Double.parseDouble(y2), roi, shape);
       }
       store.setLineText(getFirstNodeValue(textElements, "Text"), roi, shape);
     }
@@ -3311,14 +3302,14 @@ private int populateCircles(NodeList circles, int roi, int shape) {
       String centerY = getFirstNodeValue(geometry, "CenterY");
 
       if (radius != null) {
-        store.setEllipseRadiusX(DataTools.parseDouble(radius), roi, shape);
-        store.setEllipseRadiusY(DataTools.parseDouble(radius), roi, shape);
+        store.setEllipseRadiusX(Double.parseDouble(radius), roi, shape);
+        store.setEllipseRadiusY(Double.parseDouble(radius), roi, shape);
       }
       if (centerX != null) {
-        store.setEllipseX(DataTools.parseDouble(centerX), roi, shape);
+        store.setEllipseX(Double.parseDouble(centerX), roi, shape);
       }
       if (centerY != null) {
-        store.setEllipseY(DataTools.parseDouble(centerY), roi, shape);
+        store.setEllipseY(Double.parseDouble(centerY), roi, shape);
       }
       store.setEllipseText(getFirstNodeValue(textElements, "Text"), roi, shape);
     }
@@ -3544,7 +3535,7 @@ private void translateExperiment(Element root) throws FormatException {
 
         try {
           if (exposure != null) {
-            channels.get(i).exposure = DataTools.parseDouble(exposure);
+            channels.get(i).exposure = Double.parseDouble(exposure);
           }
         }
         catch (NumberFormatException e) {
@@ -3552,7 +3543,7 @@ private void translateExperiment(Element root) throws FormatException {
         }
         try {
           if (gain != null) {
-            channels.get(i).gain = DataTools.parseDouble(gain);
+            channels.get(i).gain = Double.parseDouble(gain);
           }
         }
         catch (NumberFormatException e) {
@@ -3834,7 +3825,7 @@ private void parseObjectives(NodeList objectives) throws FormatException {
 
         String lensNA = getFirstNodeValue(objective, "LensNA");
         if (lensNA != null) {
-          store.setObjectiveLensNA(DataTools.parseDouble(lensNA), 0, i);
+          store.setObjectiveLensNA(Double.parseDouble(lensNA), 0, i);
         }
 
         String magnification =
@@ -3842,7 +3833,7 @@ private void parseObjectives(NodeList objectives) throws FormatException {
         if (magnification == null) {
           magnification = getFirstNodeValue(objective, "Magnification");
         }
-        Double mag = magnification == null ? null : DataTools.parseDouble(magnification);
+        Double mag = magnification == null ? null : Double.parseDouble(magnification);
 
         if (mag != null) {
           store.setObjectiveNominalMagnification(mag, 0, i);
@@ -3851,11 +3842,11 @@ private void parseObjectives(NodeList objectives) throws FormatException {
           getFirstNodeValue(objective, "CalibratedMagnification");
         if (calibratedMag != null) {
           store.setObjectiveCalibratedMagnification(
-            DataTools.parseDouble(calibratedMag), 0, i);
+            Double.parseDouble(calibratedMag), 0, i);
         }
         String wd = getFirstNodeValue(objective, "WorkingDistance");
         if (wd != null) {
-          store.setObjectiveWorkingDistance(new Length(DataTools.parseDouble(wd), UNITS.MICROMETER), 0, i);
+          store.setObjectiveWorkingDistance(new Length(Double.parseDouble(wd), UNITS.MICROMETER), 0, i);
         }
         String iris = getFirstNodeValue(objective, "Iris");
         if (iris != null) {
@@ -4295,7 +4286,7 @@ else if (tagNode.getNodeName().equals("AcquisitionTime")) {
                     timestamp = t.asInstant().getMillis() / 1000d;
                 }
                 else if (tagNode.getNodeName().equals("ExposureTime")) {
-                  exposureTime = DataTools.parseDouble(text);
+                  exposureTime = Double.parseDouble(text);
                 }
               }
             }

From af483e7f79fc011c4adea0ab05918f374f6df348 Mon Sep 17 00:00:00 2001
From: Melissa Linkert <melissa@glencoesoftware.com>
Date: Wed, 24 Apr 2024 11:09:35 -0500
Subject: [PATCH 3/3] Use Double.parseDouble instead of DataTools.parseDouble
 to fix one more test failure

---
 .../formats-gpl/src/loci/formats/in/FlexReader.java    | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/components/formats-gpl/src/loci/formats/in/FlexReader.java b/components/formats-gpl/src/loci/formats/in/FlexReader.java
index 01c9f06de9c..fa52973495f 100644
--- a/components/formats-gpl/src/loci/formats/in/FlexReader.java
+++ b/components/formats-gpl/src/loci/formats/in/FlexReader.java
@@ -1552,7 +1552,7 @@ else if (qName.equals("Barcode")) {
       else if (qName.equals("Wavelength") && populateCore) {
         String lsid = MetadataTools.createLSID("LightSource", 0, nextLaser);
         store.setLaserID(lsid, 0, nextLaser);
-        Double wavelength = DataTools.parseDouble(value);
+        Double wavelength = Double.parseDouble(value);
         Length wave = FormatTools.getWavelength(wavelength);
         if (wave != null) {
           store.setLaserWavelength(wave, 0, nextLaser);
@@ -1566,11 +1566,11 @@ else if (qName.equals("Wavelength") && populateCore) {
         }
       }
       else if (qName.equals("Magnification") && populateCore) {
-        store.setObjectiveCalibratedMagnification(DataTools.parseDouble(value), 0,
+        store.setObjectiveCalibratedMagnification(Double.parseDouble(value), 0,
           nextObjective);
       }
       else if (qName.equals("NumAperture") && populateCore) {
-        store.setObjectiveLensNA(DataTools.parseDouble(value), 0, nextObjective);
+        store.setObjectiveLensNA(Double.parseDouble(value), 0, nextObjective);
       }
       else if (qName.equals("Immersion") && populateCore) {
         String immersion = "Other";
@@ -1656,10 +1656,10 @@ else if (qName.equals("PositionZ")) {
           }
         }
         else if (qName.equals("TimepointOffsetUsed")) {
-          planeDeltaT.add(DataTools.parseDouble(value));
+          planeDeltaT.add(Double.parseDouble(value));
         }
         else if (qName.equals("CameraExposureTime")) {
-          planeExposureTime.add(DataTools.parseDouble(value));
+          planeExposureTime.add(Double.parseDouble(value));
         }
         else if (qName.equals("LightSourceCombinationRef")) {
           lightSourceCombinationRefs.add(value);