This repository contains a Fiji/ImageJ macro toolset, that provides an interactive marker controlled watershed segmentation. This toolset uses icons comming from GIMP software, therefore icons are provided with the GIMP license (see /icons/iWatershedSeg/LICENSE).

1. install MorphoLibJ in Fiji/Imagej
2. copy iWatershedSeg.ijm and icons folder in Fiji.app/macros/toolset directory
3. copy the content of luts into Fiji.app/luts directory

1. start/load a segmentation project
2. brush tool to mark the inside of an object to be segmented
3. brush tool to mark the outside of an object to be segmented
4. eraser: reset a mark to background
5. launch the marker controlled watershed algorithm
6. record the result of watershed
7. move to one frame backward if your input data is a time serie
8. move to one frame forward if your input data is a time serie
9. extra tools like saving a project

Click on the tool 1 and choose start a new project. If your data is a volume or a time series, you must verify that your data have the appropriate dimension in Z (.e. slices) or time (i.e. nFrames). The easiest way to do that, is to use Image > Hypertstack > Hyperstack to stack tool. And if needed use Image > Hypertstack > Re-order Hyperstack ....

Select a contour map, typically the magnitude of the gradient (see Plugins > FeatureJ > FeatureJ Derivatives). In this example, the image is obtained from phase-contrast microscopy, which directly render the cells borders. Threrefore, we use the input image as contour map.

With the red brush tool (tool 2) mark the inside of your object, with the green brush tool (tool 3) mark the outside.

Run the segmntation process with tool 5.

If you are happy with the result, you can register your object, otherwise you can adjust markers with the brushes and the eraser, and re-run the watershed algorithm.

In the extral tools menu (tool 9) choose Save current project.