Nuclei Segmentation (Python)

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Type
Workflow
Author
Tosí, Sébastien
Requires
scikit-image
SciPy
NumPy
Execution Platform
Linux
Mac
Windows
Programming Language
Python
Supported image dimension
2D
Interaction Level
Automated
License/Openness
Free and open source
Description

This workflow processes images of cells with discernible nuclei and outputs a binary mask containing where nuclei are detected.

has function
Adaptative thresholding
Watershed segmentation
Object detection
Smoothing
has biological terms
nuclei
nucleus
Entry Curator
lascholz
Post date
02/26/2019 - 12:44
Last modified
05/24/2023 - 18:09
Workflow steps
Step 1: Run Gaussian Blur
Python
Image denoising
Step 2: Run Adaptive Threshold
Python
Image segmentation
Step 3: Get Euclidean Distance Transform
Python
Object feature extraction
Step 4: Run Gaussian Blur in Distance Transform
Python
Image enhancement
Step 5: Run Find Local Maxima
Python
Object detection
Step 6: Run watershed segmentation with the seeds of the local maxima
Python
Cell segmentation
Download Page
Neubias BIAFLOWS workflow of nuclei segmentation with Python
has comparison
BIAFLOWS Nuclei Segmentation project