From aee8263fd59b978db34291133e0db6ab152c1192 Mon Sep 17 00:00:00 2001 From: Antoine Weisrock Date: Fri, 29 Sep 2023 11:08:46 +0200 Subject: [PATCH 1/5] fix: fix undetected nuclei on bright multi-channel images Removes the scale-bar filter that was causing the bug. This filter wasn't essential, and processing images with a scale bar is a bad practice anyway. Signed-off-by: Antoine Weisrock --- src/myofinder/image_segmentation.py | 5 ----- 1 file changed, 5 deletions(-) diff --git a/src/myofinder/image_segmentation.py b/src/myofinder/image_segmentation.py index cbfdf4a..7cdffcb 100644 --- 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]] From 1fa021c6ce6e2da9b3c08c3276b055a4586c75b3 Mon Sep 17 00:00:00 2001 From: Antoine Weisrock Date: Fri, 29 Sep 2023 11:10:59 +0200 Subject: [PATCH 2/5] build: Update the version to 1.0.4 --- src/myofinder/__version__.py | 2 +- src/windows_installer/config.aip | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/myofinder/__version__.py b/src/myofinder/__version__.py index ba669b7..9fb71f3 100644 --- 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/windows_installer/config.aip b/src/windows_installer/config.aip index bfd3d0b..e391bf3 100644 --- a/src/windows_installer/config.aip +++ b/src/windows_installer/config.aip @@ -15,7 +15,7 @@ - + From 6baeaa66c03ccf154cf3ab055ae70d0ebc395002 Mon Sep 17 00:00:00 2001 From: Antoine Weisrock Date: Fri, 29 Sep 2023 11:20:52 +0200 Subject: [PATCH 3/5] chore: adds long_description_content_type field to setup.py --- setup.py | 1 + 1 file changed, 1 insertion(+) diff --git a/setup.py b/setup.py index 08a0c50..eaabd06 100644 --- 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 ', From 81f1a703989b6e7bb08c6a5f4d7eefbc54c29ebc Mon Sep 17 00:00:00 2001 From: WeisLeDocto Date: Fri, 29 Sep 2023 11:50:45 +0200 Subject: [PATCH 4/5] build: Windows installer now installs specific myofinder version It previously installed myofinder, it now installs myofinder==x.y.z --- src/windows_installer/start_myofinder.bat | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/windows_installer/start_myofinder.bat b/src/windows_installer/start_myofinder.bat index 1e633fb..0432ed4 100644 --- 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. From c20544b3042a99c15e32a66d1f1af678c4dc87b7 Mon Sep 17 00:00:00 2001 From: WeisLeDocto Date: Fri, 29 Sep 2023 11:52:00 +0200 Subject: [PATCH 5/5] build: update Windows installer after version update in 81f1a703 --- bin/myofinder.msi | Bin 2477568 -> 2477568 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/bin/myofinder.msi b/bin/myofinder.msi index b64a83309405298519b0e6870f3d80c2d90643f3..3931151e5f1371cb882a850e4df6220295143db4 100644 GIT binary patch delta 858 zcmXBPc}&s)90hQGLI{Xu-X<7ov^3FQN)0e7AuSJ#hQ@KJ^C`ds$$*2&;ye}|I@rcBTm_5WsROU@E4xXiwun{wpMx+1#{Sv|BaJYxS zowO`rin}F7@&GeZMezg_2KOn=*)ok#h(d8g zw!HK;>N8#D&|M?en@0*CjkgO1`b2G)?=h9xO_ zzTG<}_;;TESp0^3UH^)$?uhfi(Xl~trdz>LZdO%x;8_5Rz#MS6?&a~{9y|X;cM-g-*iKA zEL5Os#GCjbk_%zfA)fyCIWCD8)8)EL+AJQkG?*JRyzisVuOZX5jMgxDQq0f&gPt|y ztNl;zJj91Lt`mDCrY|?#e$HI;T88d3ef`M!Nz33Z)$+z(tk3L?)#oX+%7f*4TUNAk z$KM5fLsaF8;yHm0%5g=ly)IU_#<$;E(nGJ~68Pt}t+zc&c-4PWqS8mth%zgZdQaMn zJNriEy$YKdeaDP5)SwIlH*w&!s2M|}qUj~luFrPIwtP*w9}&6N6sWPp8F=+M?D4vY z7RyMzEH=nB?CQkQCb_QWG0L8S?r#6}8*V*Ho#~eutm13lBsy5i`%NvXg&WTduoi05UQer7Qb$My?r zRb^ykA^yI}$jrdNZ~}-yz&F_04Mh7)=RBpVT+hq~;(&m5c-kZdhT@XMqLTRB%KWs< zyp+@;y`;nv23^PhH@`44vpIWD4N1(tZ6NSB??e3#wn=L*ugi_E?f(Am=iGJcANpms9IE0_vC-VzB;UJtxB2!L zj`flP8^Y#gEo9^kzZR0AQTJnM&z9K})G|M@e!kSC+x0_eLc%ui&GjGW!=YO7`dzR@iEYGZ2 zk#km^e~a8pC6oH@DZba=o|ut*Ve;m8m%<&j)8p?iIjL%8BILVnhEGLJXZox+=4Ynu z4DWOL=JaL?v+UWMMfZAmo+O5unqAuyas2wjhb&(Ys`W4}vb24X6n^Yw#gsy~5TxzRn!rcFVx}q(s%Ju_V%o7;_mcU?<