nuclei

Clustered Cell Nuclei Data

Submitted by Perrine on Mon, 08/26/2019 - 11:24

One of the principal challenges in counting or segmenting cells or cell nuclei is dealing with clustered objects. To help assess algorithms' performance in this regard, synthetic 3D image sets of HL60 cell line are provided consisting of four subsets with increasing degree of clustering. Each subset is also provided in two diferent levels of quality: high SNR and low SNR. Ground truth is available as well.

Nuclei Segmentation (ilastik)

Workflow
Description

NEUBIAS-WG5 workflow for nuclei segmentation using ilastik v1.3.2 and Python post-processing.

has topic
Machine learning
has function
Pixel classification
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Nuclei Segmentation (CellProfiler)

Workflow
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

Nuclei Tracking (ImageJ)

Workflow
has function
Object tracking
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Nuclei Segmentation (Python)

Workflow
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
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