Update SciJava Ops FLIM README

Author: gselzer

scijava-ops-flim/README.md

@@ -1,12 +1,70 @@
-# SciJava Ops Flim: A fluorescence lifetime analysis library for SciJava Ops.
+# SciJava Ops FLIM: A fluorescence lifetime analysis library for SciJava Ops.
 
-This library provides a bridge between SciJava Ops and Flim.
-For Maven projects, this library can be used by adding to your `pom.xml`:
+SciJava Ops FLIM is a collection of FLIM analysis ops based on [FLIMLib](https://github.com/flimlib/flimlib). It extends the single-transient fitting functions in FLIMLib to dataset-level fitting ops. Currently supported fitting ops include: RLD, MLA, Global, Phasor, and single-component Bayesian.
 
-```java
-<dependency>
-	<groupId>org.scijava</groupId>
-	<artifactId>scijava-ops-flim</artifactId>
-	<version>0-SNAPSHOT</version>
-</dependency>
+Besides curve fitting, SciJava Ops FLIM also provides a variety of pre-processing options such as pixel binning, intensity thresholding, ROI masking as well as post-processing utility ops for e.g. calculating τ<sub>m</sub> (mean lifetime), A<sub>i</sub>% (fractional contribution) and pseudocoloring the result with LUT.
+
+# Example usage
+Open [test2.sdt](test_files/test2.sdt) in [Fiji](https://fiji.github.io/). Execute in [Script Editor](http://imagej.github.io/Using_the_Script_Editor) as Groovy:
+
+```groovy
+#@ UIService ui
+#@ OpEnvironment op
+#@ ImgPlus img
+
+// set up parameters
+import org.scijava.ops.flim.FitParams
+
+param = new FitParams()
+param.transMap = img; // input 3-dimensional (x, y, t) dataset
+param.xInc= 0.040     // time difference between bins (ns)
+param.ltAxis = 2      // time bins lay along axis #2
+
+// op call
+fittedImg = op.unary("flim.fitLMA").input(param).apply().paramMap
+
+// display each parameter
+zImg = op.ternary("transform.hyperSliceView").input(fittedImg, param.ltAxis, 0L).apply()
+AImg = op.ternary("transform.hyperSliceView").input(fittedImg, param.ltAxis, 1L).apply()
+tauImg = op.ternary("transform.hyperSliceView").input(fittedImg, param.ltAxis, 2L).apply()
+
+ui.show("z", zImg)
+ui.show("A", AImg)
+ui.show("tau", tauImg)
+```
+
+After running this script, the output shown below can be seen by first running the script, and then brightness and contrast (Ctrl + Shift + C, select "Set" and bound the contrast to each image's corresponding range below).
+
+(z in [-1, 1], A in [0, 4], tau in[0, 3]):
+
+![example output](images/example%20z.png)![example output](images/example%20A.png)![example output](images/example%20tau.png)
+
+See more examples in [Demo.ipynb](notebooks/Demo.ipynb) and [groovy.md](groovy.md).
+
+# Using from a Java project
+
+To depend on SciJava Ops FLIM, copy the following to your `pom.xml`:
+
+```xml
+  <properties>
+    <scijava-ops-flim.version>0-SNAPSHOT</scijava-ops-flim.version>
+  </properties>
+
+  <dependencies>
+    <dependency>
+      <groupId>org.scijava</groupId>
+      <artifactId>scijava-ops-flim</artifactId>
+      <version>${scijava-ops-flim.version}</version>
+    </dependency>
+  </dependencies>
 ```
+
+# See also
+
+- [FLIMLib](https://github.com/flimlib/flimlib): Curve fitting library for FLIM
+    - [Debug tutorial](https://github.com/flimlib/flimlib/wiki/Debugging)
+- [FLIMJ Ops](https://github.com/flimlib/flimj-ops): ImageJ Ops for accessing FLIM
+
+# Citation
+
+Comming soon...