How to Create a Polygon (ROI) file

Fiji is an open-source image processing package that includes many useful plugins for scientific image analysis. For more information and/or to download Fiji, visit the official Fiji website.

Please follow these steps to create a polygon region in Fiji:

1. Click on Plugins in the menu bar.


2. Navigate to ThunderSTORM -> Import/Export -> Import results.

   
   

   
   
3. Ensure the file format is set to CSV.

   
   

   
   
4. Click the button with the ... icon to navigate to the file path containing your detection file.

   
   

   
   
5. Locate your CSV detection file and click OK.

   
   

   
   
6. You will be brought back to the Import Results menu. Click OK again.


7. Click on Visualisation.

   
   

   
   
8. Set these top values to 0 and click OK.

   
   

   
   
9. Select the Polygon Tool and draw around the cell.

   
   

   
   
10. Right-click on the cell and select ROI Properties….

    
    

    
    
11. Tick the checkbox for List coordinates and click OK.

    
    

    
    
12. Right-click the window displaying the list of coordinates and select Save As….

    
    

    
    
13. Save the file in the same directory as your detection file and name it: {DETECTION_FILE_NAME}_ROI.csv.