Nuclei Segmentation (CellProfiler)

Type
Workflow
Author
Paavolainen, Lassi
Requires
CellProfiler
Execution Platform
Linux
Mac
Windows
Implementation Type
plugin
Programming Language
CellProfiler Pipeline
Supported image dimension
2D
Interaction Level
Automated
License/Openness
Free and open source
Description

This workflow processes a group of images containing cells with discernible nuclei and segments the nuclei and outputs a binary mask that show where nuclei were detected. It was developed as a test workflow for Neubias BIAFLOWS Benchmarking tool.

has function
Image segmentation
has biological terms
nucleus
nuclei
Entry Curator
czhang
Post date
02/27/2019 - 14:58
Last modified
05/17/2023 - 14:45
Workflow steps
Step 1: Smoothing input image
CellProfiler Smooth
Smoothing
Step 2: Thresholding input image
CellProfiler Threshold
Image thresholding
Step 3: Run LoG on input image
CellProfiler
Image feature detection
Step 4: Find Maxima in LoG image
IdentifyPrimaryObjects
Object detection
Step 5: Declump using Propagate
Nuclei Segmentation (CellProfiler)
Cell segmentation
Download Page
Neubias BIAFLOWS workflow of nuclei segmentation with CellProfiler pipeline
has comparison
BIAFLOWS Nuclei Segmentation project