Learn how to use FIJI (ImageJ) to separate objects that are touching, merged, connected or are clustered by using various watershed algorithms. Watershed procedures generate either binary or label images of the separated objects. Counting of these objects can be done with the Particle Analyzer (Analyze Particles) or using the ROI Manager or 3D Manager. Examples are shown for 2D and 3D (z-stack) images.
0:00 Introduction/ 2D Image
0:52 Standard Binary Watershed
1:29 MorphoLibJ's Distance Transform Watershed
3:32 3D Suite's 3D Watershed Split
4:11 3D Suite's 3D Watershed
5:30 SCF's Interactive H_Watershed
6:48 StarDist (2D)
7:22 3D or Z-stack Images
The following plugins/update sites were used in this video:
IJPB-plugins : MorphoLibJ
3D ImageJ Suite and ImageScience
SCF-MPI-CBG
PTBIOP
StarDist and CSBDeep
*Bubble image stack (original non-binary image) credit: Scott Moyer
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