Nuclei Segmentation 3D Watershed (NucleiSegmentation3D-ImageJ)

need a thumbnail
Type
Workflow
Author
Tosí, Sébastien
Requires
ImageJ
Execution Platform
Linux
Mac
Windows
Implementation Type
plugin
Programming Language
ImageJ Macros
is compatible with
ImageJ Macro
Supported image dimension
3D
Interaction Level
Automated
License/Openness
Free and open source
Description

The macro will segment nuclei and separate clustered nuclei in a 3D image using a distance transform watershed. As a result an index-mask image is written for each input image.

has function
Image segmentation
Watershed segmentation
Smoothing
Entry Curator
czhang
Post date
02/05/2019 - 15:38
Last modified
05/24/2023 - 18:34
Workflow steps
Step 1: Compute Gaussian Blur
Gaussian Blur 3D (ImageJ)
Image denoising
Step 2: Threshold image
ImageJ Built-in Macro Functions
Image segmentation
Step 3: 3D Fill holes
3D ImageJ Suite
Morphological operation
Step 4: Compute Distance Transform Watershed 3D
MorphoLibJ
Cell segmentation
Step 5: Label connected components
MorphoLibJ
Object counting
Download Page
Neubias BIAFLOWS workflow of nuclei segmentation 3D with ImageJ
has comparison
BIAFLOWS NUCLEI-SEGMENTATION-3D