3D Slicer for annotating microscopy data

Demonstration of using 3D Slicer to annotate individual neurons/cells in a 3D image stack acquired using a confocal microscope. The labels are then exported as binary labelmaps, and subsequently imported into ImageJ/FIJI. 3D Slicer: https://www.slicer.org/ Used v 4.10.2 in this video Tutorials: https://www.slicer.org/wiki/Documenta... FIJI: https://fiji.sc/ MorphoLibJ plugin in FIJI: https://imagej.net/MorphoLibJ 3D ImageJ suite in FIJI: https://imagej.net/3D_ImageJ_Suite 0:00 Start 1:55 Importing stack 4:59 Filtering/Denoising 6:00 Segmentation Editor and adding ROIs 7:27 Labelling cells 10:00 Level trace tool for labelling 14:30 Overlapping labels 21:45 Grow from Seeds 25:00 Filtering and Smoothing labels 27:00 Exporting label data as tif 29:00 Importing label data into ImageJ/FIJI