Fos Protein and c-fos mRNA Manual Counts for Quanty-cFOS.ijm Validation

This repository contains the ImageJ/Fiji GT_Annotations.ijm tool and representative Fos/c-fos stained images that can be used to validate the Quanty-cFOS automated counting tool for Fos protein and c-fos mRNA

How to run the GT-Annotations_v0.ijm tool

The user can open the GT_Annotations.ijm by dragging and dropping the file on the main ImageJ/Fiji window. This opens the ImageJ/Fiji interpreter that can be used to run the code. Alternatively, you can copy the file in the ImageJ/Fiji plugin directory and run the tool using the ImageJ/Fiji GUI (e.g.: C:\Users\XXX\XXX\XXX\fiji-win64\Fiji.app\plugins). Please, restart ImageJ/Fiji after this operation

Step-by-Step Instructions:

1. Hit the Run button or go to plugin and select GT-Annotations_v0
2. Select the input file to process from the SampleImages folder
3. A dialog box will pop up
4. Enter your fist name and press ok
5. Use the left mouse button to mark positive cells and the right mouse button to label negative cells. The cells are marked in 2 different colors depending on the image lookup table
6. To finish the annotation step hit the shift key on your keyboard
7. The dialog box will pop up again
8. To end the annotation task check the box End annotating and uncheck the box Start annotating. If there is a need in annotating a different channel on the input image the user can start a new round of annotations. In this case the ID changes of one unit for later postprocessing

The output folder is saved in the input folder and it contains:

1. The image with the overlaid labels
2. The ROIs added to the RoiManager
3. A csv file with the annotation ID, the xy coordinates of the center of mass, the class index (1: positive, 3: negative) and the class name (cFOS positive or negative)
4. A Log file

Please let me know if you have any suggestion on how to improve the tool or if you think some functionalities are missing