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.

Nuclei Segmentation 2D watershed (NucSeg3DThr-ImageJ)

Workflow
Description

The macro will segment nuclei and separate clustered nuclei in a 3D image using a 2D Gaussian blur, followed by Thresholding, 2D hole filling and a 2D watershed. As a result an index-mask image is written for each input image.

has topic
Bioimage informatics
has function
Cell segmentation
Watershed segmentation
Morphological operation
need a thumbnail

Nuclei Segmentation (U-Net)

Workflow
Description

U-Net segmentation as presented in Reference Publication. The model predicts three classes: background, edge and foreground. The model was trained with Kaggle Data Science Bowl (DSB) 2018 training set.

has topic
Machine learning
has function
Cell segmentation
need a thumbnail

Nuclei Segmentation (DeepCell)

Workflow
Description

Nuclei Segmentation using Deep Learning for individual cell analysis (DeepCell).

has topic
Machine learning
has function
Cell segmentation
need a thumbnail

Spot Detection 3D Hessian (ImageJ)

Workflow
Description

3D spot detection using the Determinant of Hessian (DoH) and the detection of 3D minima.

has topic
Bioimage informatics
has function
Spot detection
Feature enhancement
need a thumbnail

Spot Detection 3D (Icy)

Workflow
Description

Spot detection in 3D images by Wavelet Adaptive Threshold in Icy.

has function
Spot detection
need a thumbnail
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