Object Tracking (MU-Lux-CZ)

Description

Cell tracking using MU-Lux algorithm.

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Object Tracking (Octave)

Description

Nuclei tracking in 2D time-lapse with Octave tracker (adapted from Matlab LOBSTER version.

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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 (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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Nuclei Segmentation (DeepCell)

Description

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

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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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NucleusJ

Description

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Starting from image stacks, the nuclear boundary as well as nuclear bodies are segmented. As output, NucleusJ automatically measures 15 parameters quantifying shape and size of nuclei as well as intra-nuclear objects and the positioning of the objects within the nuclear volume.

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Amira / Avizo Xtra library

Description

Collection of add-ons (recipes, scripts, demos,…) that will help you improve your day-to-day use of Amira-Avizo and PerGeos Software and make you gain both time and efficiency.
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