Merge branch 'master' of https://github.com/computational-cell-analyt…

…ics/micro-sam into bioengine

.github/workflows/build_installers.yaml

@@ -27,7 +27,7 @@ jobs:
       RUN_SCRIPT: |
         python version_getter.py
         mkdir ./${{ matrix.os }}_x86_64
-        constructor --output-dir ./${{ matrix.os }}_x86_64 .
+        constructor --output-dir ./${{ matrix.os }}_x86_64 --config-filename construct_${{ matrix.os }}.yaml . 
 
     steps:
       - name: checkout

deployment/construct_windows-latest.yaml

@@ -0,0 +1,14 @@
+name: micro_sam
+version: 0.0.1
+license_file: ../LICENSE
+installer_type: pkg  #[osx]  # This will trigger pkg build on Mac Os. On windows and linux, native build will be done and this has no effect.
+environment: __MICROSAM_BUILD_ENV__
+welcome_image: ../doc/logo/logo.png
+header_image: ../doc/logo/logo.png
+icon_image: ../doc/logo/logo.png
+channels:
+  - conda-forge
+welcome_text: Install Segment Anything for Microscopy.
+conclusion_text: Segment Anything for Microscopy has been installed.
+initialize_by_default: false
+post_install: post_install.bat

deployment/post_install.bat

@@ -0,0 +1,49 @@
+@echo off
+
+rem This script searches for the 'freetype.dll' file within a specific directory 
+rem and attempts to move it to the target directory during post-installation on Windows.
+rem If not found locally, it downloads the DLL from a defined URL.
+
+
+rem Define download URL (replace with the actual URL for your desired version)
+set DOWNLOAD_URL=https://raw.githubusercontent.com/ubawurinna/freetype-windows-binaries/master/release%20dll/win64/freetype.dll
+
+rem Define target directory within the installation prefix
+set TARGET_DIR=%PREFIX%\Scripts
+
+rem Create the target directory if it doesn't exist
+if not exist "%TARGET_DIR%" mkdir "%TARGET_DIR%"
+
+rem Search for freetype.dll in specific directory (adjust path as needed)
+for /F "tokens=*" %%a in ('dir /S /B "%PREFIX%\Library\freetype.dll"') do (
+  if exist "%%a" (
+    echo Found freetype.dll in %%a
+    move "%%a" "%TARGET_DIR%"
+    if exist "%TARGET_DIR%\freetype.dll" (
+      echo Moved freetype.dll to %TARGET_DIR%
+      exit /b 0  ; Exit script with success code if moved
+    ) else (
+      echo Error: Failed to move freetype.dll (check permissions)
+      exit /b 1  ; Exit script with error code
+    )
+  )
+)
+
+rem If not found in specific location, proceed with download
+powershell -ExecutionPolicy Bypass -Command Invoke-WebRequest -Uri %DOWNLOAD_URL% -OutFile "%TARGET_DIR%\freetype.dll"
+
+if exist "%TARGET_DIR%\freetype.dll" (
+  echo Downloaded freetype.dll to %TARGET_DIR%
+) else (
+  echo Error downloading freetype.dll
+  rem Attempt to download the DLL again (optional)
+  powershell -ExecutionPolicy Bypass -Command Invoke-WebRequest -Uri %DOWNLOAD_URL% -OutFile "%TARGET_DIR%\freetype.dll"
+  if exist "%TARGET_DIR%\freetype.dll" (
+    echo Retry: Downloaded freetype.dll to %TARGET_DIR%
+  ) else (
+    echo Error: Failed to download freetype.dll even after retry
+    exit /b 1  ; Exit script with error code after retries
+  )
+)
+
+exit /b 0  ; Exit script with success code (after download if necessary)

micro_sam/napari.yaml

@@ -1,8 +1,9 @@
 name: micro-sam
 display_name: SegmentAnything for Microscopy
+# see https://napari.org/stable/plugins/manifest.html for valid categories
+categories: ["Segmentation", "Annotation"]
 contributions:
   commands:
-
     # Commands for sample data.
     # We don't provide the sample data for image series via napari for now,
     # because the image series annotator cannot be called for image layers in napari (yet),

notebooks/README.md

@@ -1,4 +1,4 @@
-# Example Noteboks
+# Example Notebooks
 
 We provide three example notebooks that demonstrate how the `micro_sam` python library can be used for:
 - Running automatic instance segmentation in `automatic_segmentation.ipynb`.