cellDistanceClassification

This groovy script helps to quantify min distances among cells to classify them into single, nearby attached and umbrella cells. Moreover, two additional groovy scripts (doublePositiveCellQuantification.groovy, singlePositiveCellQuantification.groovy) are provided in order to quantify single, and double positive- negative cells.

Download cellDistanceClassification 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

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

ImageJ-win64.exe --ij2 --headless --run "/absolute_path/to/groovyscript/cellDistanceClassification.groovy" "headless=true, inputFilesDir='/absolute_path/to/inputFiles/images',outputDir='/absolute_path/to/outputDirectory/results',gfpModel='/absolute_path/to/gfpModel',greenChannel=1"

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'
• gfpModel : Absolute path to file containing GFP model for segmentation. /home/anaacayuela/Ana_pruebas_imageJ/models/model_gfp
• greenChannel : Channel in which GFP marker is located 1

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.