Merge pull request #12 from TissueEngineeringLab/11-obvious-nuclei-no…

…t-being-detected 11 obvious nuclei not being detected
TissueEngineeringLab · Sep 29, 2023 · 0c54c52 · 0c54c52
2 parents b27251f + c20544b
commit 0c54c52
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Showing 6 changed files with 4 additions and 8 deletions.
diff --git a/bin/myofinder.msi b/bin/myofinder.msi
diff --git a/setup.py b/setup.py
@@ -27,6 +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',
   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__ = '1.0.3'
+__version__ = '1.0.4'
diff --git a/src/myofinder/image_segmentation.py b/src/myofinder/image_segmentation.py
@@ -62,11 +62,6 @@ def __call__(self,
             raise IOError("Could not load the image for segmentation, "
                           "aborting !")
 
-        # Removing the scale bar
-        image[(image[:, :, 0] > 50) &
-              (image[:, :, 1] > 50) &
-              (image[:, :, 2] > 50)] = (0, 0, 0)
-
         nuclei_channel = image[:, :, colors[0]]
         fiber_channel = image[:, :, colors[1]]
 

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="1.0.3" Options="32"/>
+    <ROW Property="ProductVersion" Value="1.0.4" 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
+    %base_path%\venv\Scripts\python -m pip install myofinder==1.0.4
 )
 
 echo.