fluorescenceQuantification_code

This Groovy script helps to quantify fluorescence intensity statistics in Nuclei and cytoplasm

Download fluorescenceQuantification_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 fluorescenceQuantification_code in headless mode through ImageJ/Windows Windows Terminal (ALL parameters)

ImageJ-win64.exe --ij2 --headless --run "/absolute_path/to/groovyscript/fluorescenceQuantification.groovy" "headless=true, inputFilesDir='/absolute_path/to/inputFiles/images',outputDir='/absolute_path/to/outputDirectory/results',applyDAPI=false,"

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'

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: fluorescenceQuantification.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 (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 (twoCSV table corresponding for each analysis: per slice and per image (or serie)) in the output directory previously selected.