Imagej Plugin for supporting manual mask annotation using ROI Manager in ImageJ/Fiji
Download file from Download_Link
Place .jar file in Fiji.app>Plugins folder
Start Fiji
Quick Save Mask can be found in Plugins Menu of ImageJ/Fiji or type to search in the search textbox
Select the Plugin Quick Save Mask in the Plugin Menu
Use the Browse Button to select the output folder
Output Suffix: predefine a suffix for the mask output.
Enable “Save ROIs as ZIP file” to store all ROIs from the ROI Manager in a single ZIP file, allowing you to reload your work later and continue where you left off.
Click Ok
The ROI Manager will be opened and should be kept open while working, as it manages all your selections.
Open an image of your choice using ImageJ/Fiji
Using one of the selection tool to draw the contour of your mask
Press T on keyboard or Add Button in the ROI Manager to add selection to ROI Manager
Continue to draw and add until you want to save; Using the ROI Manager to remove or find a specific selection(Go to ImageJ ROI Manager for more information)
When you want to save ,press the Quick Save Mask Button
Move your mouse on top of the Image and click 1 time
The plugin should create a new binary mask image with all of your selection (255 is the foreground and 0 is the background) and save to output folder
If needed, double click on the Quick Save Mask Button to open the setting dialog and adjust, click ok to save setting, cancel to not save any changes.