Protocol

Detection (with cluster un-mixing) and tracking of neurons with EMC2

Publication ID: ICY-77886

Short Description

This protocol

1- detects bright spots (neurons) with Wavelet spot detector

2- un-mix (i.e. detects individual spots in large clusters) with Laplacian of Gaussian (LoG) convolution & local maxima detection

3- Tracks spots (neurons) with enhanced Multiple-Hypothesis-Tracking (eMHT) implemented in the Spot Tracking blocks

4- Close tracking gaps with EMC2

This protocol can be slow, with a high computational load for large & long time lapse sequences due to the convolution and local maxima steps. For long/large movies, the protocol http://icy.bioimageanalysis.org/protocol/detection-and-tracking-of-neurons-with-rmc2/ should be preferred.

Team: BioImage Analysis Unit
Institution: Institut Pasteur
Website: https://research.pasteur.fr/fr/team/bioimage-analysis/preprint: https://www.biorxiv.org/content/10.1101/2020.06.22.165696v1.abstract

Documentation

Please refer to the documentation of

Spot detector http://icy.bioimageanalysis.org/plugin/spot-detector/

Spot tracking http://icy.bioimageanalysis.org/plugin/spot-tracking/

and

EMC2 http://icy.bioimageanalysis.org/plugin/elastic-motion-correction-concatenation-emc2-of-tracks/

for more details

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Changelog

  • Version 1 • Released on: 2020-07-02 00:00:00
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