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.

Object Tracking (ImageJ)

Description

Object tracking. For each time-frame, an image mask is obtained from median filtering (user defined radius), thresholding (user defined level) and hole filling. Convex objects are split apart by distance map watershed from regional intensity maxima (user defined noise tolerance), eroded (user defined radius) and analyzed as 3D particles (assuming some overlap between objects from a frame to the next frame). Finally, division events are analyzed and accounted for to relabel objects.

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Nuclei Tracking (TrackMate)

Description

Track non-dividing particles in 2D time-lapse image.

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Particle Tracking (ImageJ)

Description

Particle tracking in 2D time-lapse based on linking closest regional intensity minima (user defined noise tolerance) detected from Laplacian of Gaussian filtered images (user defined radius). A maximum linking distance is set (user defined).

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Nuclei Segmentation 3D (Ilastik)

Description

Execute Nuclei Segmentation in 3D images using pixel classification with ilastik.

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Nuclei Segmentation 3D watershed (ImageJ)

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.

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Nuclei Segmentation (U-Net)

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.

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Spot Detection 3D Hessian (ImageJ)

Description

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

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Spot Detection 3D (Icy)

Description

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

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Spot Detection Dmap (ImageJ)

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).

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3D cell tracking using Gaussian Mixture Model (TGMM)

Description

TGMM is a cell tracking solution for large 3D volume (typically lightsheet).

It detects cell nuclei by fitting gaussians on their fluorescent intensity.

It can run on GPU using CUDA and is called via the command line.

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