Workflow

A workflow is a set of components assembled in some specific order to

  1. Measure and estimate some numerical parameters of the biological system or
  2. Visualization

for addressing a biological question. Workflows can be a combination of components from the same or different software packages using several scripts and manual steps.

Landmark detection MSET models training

Workflow
Description

This workflow trains MSET landmark detection models from a dataset of annotated images.

has topic
Machine learning
has function
Landmark assignment
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Pixel classification for GlaS challenge with UNet

Workflow
Description

This workflow segments glands from H&E stained histopathological images
from the Gland Segmentation Challenge (GlaS2015) using deep learning (UNet).
UNet implementation largely inspired from PyTorch-UNet by Milesial. 

has function
Pixel classification
Smoothing
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VascuSynth

Workflow
Description

VascuSynth is an ITK-based synthetic image generator. It synthesizes volumetric images of vascular trees and generates a .gxl file of the ground-truth tree structure. VascuSynth receives a number of .txt configuration files and is capable of generating both ground truth ('ideal') images and images with added noise. The user is capable of choosing from a set simple noise additions and artefacts.

has function
Image generation

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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