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.

Nuclei Segmentation (ilastik)

Description

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

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Nuclei Segmentation (Mask-RCNN)

Description

NEUBIAS-WG5 workflow for nuclei segmentation using Mask-RCNN. The workflow uses Matterport Mask-RCNN. Keras implementation. The model was trained with Kaggle 2018 Data Science Bowl images.

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Landmark detection DMBL model prediction

Description

This workflow predict landmark positions on images by using DMBL landmark detection models.

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Landmark detection DMBL model training

Description

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

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Landmark detection LC models prediction

Description

This workflow predict landmark positions on images by using LC landmark detection models.

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Landmark detection LC models training

Description

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

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Landmark detection MSET models prediction

Description

This workflow predict landmark positions on images by using MSET landmark detection models.

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Landmark detection MSET models training

Description

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

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Pixel classification for GlaS challenge with UNet

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. 

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VascuSynth

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.

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