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 (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

Spot Detection Dmap (ImageJ)

Workflow
Description

This workflow detects spots in a 2D image by filtering the image by Laplacian of Gaussian (user defined radius), thresholding (user defined threshold) and finding local intensity maxima in mask distance map (Dmap).

has function
Spot detection
Distance transform
need a thumbnail
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