2DColocGfpKi67_code

This groovy script helps to quantify 2D Colocalization GFP/ki67+. One groovy script (2DColocGfpKi67_code.groovy) is provided in order to quantify Total DAPI, Total GFP+, Total GFP-Ki67+

Download c2DColocGfpKi67_code

1. Go to the GitHub repository
2. Click on <Code>>Download ZIP
3. The repo will be found at Downloads directory.

Please note that you must have installed the IJPB-Plugins library in ImageJ UpdateSite:

1. Click on Help>Update

Please note that you must have installed the PTBIOP library in ImageJ UpdateSite:

1. Click on Help>Update

Please note that you must have the conda Cellpose environment configured in Cellpose wrapper :

NOTE The Fiji - Cellpose wrapper is useless without a working Cellpose environment, please see installation abobe (I.A.). To test if you have a working Cellpose environment: 1 - Activate your environment 2 - Type python -m cellpose --help You should not get an error.

• Plugins>BIOP>Cellpose>Cellpose setup...``
• Select the path to your working Cellpose virtual environment
• Select EnvType : conda or venv
• Select version : 0.6 , 0.7 , 1.0 or 2.0.

• 

• Restart Fiji

Running 2DColocGfpKi67_code in headless mode through ImageJ/Windows Windows Terminal (ALL parameters)

ImageJ-win64.exe --ij2 --headless --run "/absolute_path/to/groovyscript/2DColocGfpKi67_code.groovy" "headless=true, inputDir='/absolute_path/to/inputFiles/images',outputDir='/absolute_path/to/outputDirectory/results',dapiChannel=0,greenChannel=1,redChannel=2"

Parameters Explanation:

• headless : true.
• inputFilesDir : Directory in which the images (tiff, jpeg... files) to be analyzed are located. '/home/anaacayuela/Ana_pruebas_imageJ/margarita/images'.
• outputDir : Directory in which the outputs are saved. '/home/anaacayuela/Ana_pruebas_imageJ/margarita/results'
• dapiChannel : Channel in which DAPI is located 0
• greenChannel : Channel in which GFP marker is located 1
• redChannel : Channel in which ki67 marker is located 2

Running through ImageJ/Fiji

1. Navigate to reach Script Editor tool:

   • By writing true on the search tool or by File>New>Script...

   

2. Browse to find the directory in which the corresponding the groovy script is stored: cellDistanceClassification.groovy

   

3. Press Run button to compile the script.

   

4. Then a dialog will be displayed in order to set both the input directory path in which the images (not ready to deal with LIF files) to be analyzed are stored and the output directory path to save the outputs.

   

5. A log window will appear to update about the processing status.

6. Finally, you will be enabled to check the outputs (oneCSV table corresponding to each image located in the output directory previously selected.