Merge pull request #13 from TissueEngineeringLab/v1.0.5

Improvement of segmentation performance
TissueEngineeringLab · Oct 2, 2023 · 5ba2103 · 5ba2103
2 parents 0c54c52 + d5ee3e1
commit 5ba2103
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Showing 6 changed files with 10 additions and 10 deletions.
diff --git a/bin/myofinder.msi b/bin/myofinder.msi
diff --git a/setup.py b/setup.py
@@ -27,7 +27,7 @@
   of them, visualizing the output, and manually correcting it if needed. It 
   relies on the DeepCell library for performing the image segmentation.
   """,
-  long_description_content_type='text/plain',
+  long_description_content_type='text/x-rst',
   keywords='segmentation,fusion index,automation,muscle culture',
   license='GPL V3',
   classifiers=['Development Status :: 5 - Production/Stable ',

diff --git a/src/myofinder/__version__.py b/src/myofinder/__version__.py
@@ -1,3 +1,3 @@
 # coding: utf-8
 
-__version__ = '1.0.4'
+__version__ = '1.0.5'
diff --git a/src/myofinder/image_segmentation.py b/src/myofinder/image_segmentation.py
@@ -67,16 +67,16 @@ def __call__(self,
 
         del image
 
-        # Default parameters
-        radius = 10
-        maxima_threshold = 0.1
-        interior_threshold = 0.01
+        # Segmentation parameters
+        radius = 2
+        maxima_threshold = 0.05
+        interior_threshold = 0.3
         maxima_smooth = 0
-        interior_smooth = 0
+        interior_smooth = 2
         maxima_index = 0
         interior_index = -1
         label_erosion = 0
-        fill_holes_threshold = 0
+        fill_holes_threshold = 15
         pixel_expansion = None
         maxima_algorith = 'h_maxima'
 

diff --git a/src/windows_installer/config.aip b/src/windows_installer/config.aip
@@ -15,7 +15,7 @@
     <ROW Property="ProductCode" Value="1033:{BFA51019-B48F-475B-B8BB-E2F14499079C} " Type="16"/>
     <ROW Property="ProductLanguage" Value="1033"/>
     <ROW Property="ProductName" Value="MyoFInDer"/>
-    <ROW Property="ProductVersion" Value="1.0.4" Options="32"/>
+    <ROW Property="ProductVersion" Value="1.0.5" Options="32"/>
     <ROW Property="SecureCustomProperties" Value="OLDPRODUCTS;AI_NEWERPRODUCTFOUND"/>
     <ROW Property="UpgradeCode" Value="{CE95562D-8E91-4ED9-B26E-5638FFE5C0B0}"/>
     <ROW Property="WindowsType9X" MultiBuildValue="DefaultBuild:Windows 9x/ME" ValueLocId="-"/>

diff --git a/src/windows_installer/start_myofinder.bat b/src/windows_installer/start_myofinder.bat
@@ -41,7 +41,7 @@ echo Checking if the dependencies are installed
     echo The dependencies are installed
 ) || (
     echo The dependencies are not installed, installing them
-    %base_path%\venv\Scripts\python -m pip install myofinder==1.0.4
+    %base_path%\venv\Scripts\python -m pip install myofinder==1.0.5
 )
 
 echo.