Labkit is a Fiji-plugin which allows one to prepare instance masks for your images.

• Start Fiji
• Select Help>Update
• Select Labkit after clicking on Manage Update Sites
• Select Close, Apply changes and Ok
• Restart Fiji
• Open an image which you would like to annotate
• Search for Labkit in the Fiji search bar

• Ensure that override is selected
• Select + Add label
• Use the Draw button (pencil icon) to mark the contour around any one object instance
• Use the Flood Fill button (bucket icon) to fill inside this contour
• When all objects have been labeled in the manner above, select Labeling>Show Labeling in ImageJ (this pops an instance mask where each object is labeled with a unique id)
• Use File > Save As > Tiff in the Fiji menu bar to save your instance mask