marker controlled Watershed

clij / clijx

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marker controlled Watershed #17

Open haesleinhuepf opened 3 years ago

haesleinhuepf commented 3 years ago

Suggested by @pr4deepr

''' Marker controlled watershed from MorpholibJ If I am using CLIJx to generate seeds (labelling) and binary images (mask), then if I have edges image I can use these images for segmenting cells using Marker Controlled Watershed. '''

haesleinhuepf commented 3 years ago

Hey @pr4deepr ,

have you tried https://clij.github.io/clij2-docs/reference_seededWatershed

Thanks!

pr4deepr commented 3 years ago

I just tried it.

Top row is seeded watershed: The input image from CLIJx assistant, followed by labelling workflow ALX and then seeded watershed in CLIJx.
Bottom row is marker controlled watershed: the edges image (Canny-Deriche) and binary image with same threshold specified as in CLIJx assistant. The final labelled image is on the right.

The labelling wasn't optimised as much, but this demonstrates the differences.

haesleinhuepf commented 3 years ago

Awesome! I can see the issue now. Does it also fail in 2D? Can you share the dataset and the script which generates both results? That would make it easy for me to trace it down in more detail.

pr4deepr commented 3 years ago

I haven't tried 2D.

Yup, happy to share the dataset. Both the image and the macro is in this folder.