matlab_tirfm_movies
Science Score: 57.0%
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✓CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
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✓DOI references
Found 1 DOI reference(s) in README -
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○Scientific vocabulary similarity
Low similarity (6.2%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: DietzlabTUM
- License: gpl-3.0
- Language: MATLAB
- Default Branch: main
- Size: 198 KB
Statistics
- Stars: 4
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 1
Metadata Files
README.md
matlabtirfmmovies
These and other related scripts were written by Dr. Matthias Schickinger, Dr. Philip Ketterer, Dr. Jonas Funke, Anna-Katharina Pumm, Dr. Wouter Engelen and Eva Bertosin
The main scripts are in matlabtirfmmovies folder, named from 1 to 5.
1-processmoviesmanual: load movies, compute STD DEV of whole movie, pick and export all particles (spots) To change: run('/Users/username/Documents/MOVIE_TIRFM/functions/startup.m')
2-getstddevofspots: calculate STD DEV of all spots to change: folders to load spots
3-classifysumtifs: classification of all spots according to their STD DEV (classes: stationary, diffusive, moving, unclear) only "moving" spots will be further processed
4-analysesortedparticles: find center of spots, fit PSF to spots, find spots in each frame with VWCM to change: folders to load spots
5-classify_spots: classify moving spots into switching between 2 or 3 positions, stationary, rotating, diffusive (no full circle) and unclear calculate RMSD, cumulative angle, angular traces, angular velocity, distance from center for desired type of spots (switching, rotating, diffusive)
For TIRM movies that haven't been fitted with the above-named matlab scripts, but for example with the open source Picasso software (https://github.com/jungmannlab/picasso) an alternative main script is available:
classifyspotseField: only for movies with an applied external AC fied import fitted spots from hdf5 files and classify spots calculate histograms of netto rotations and cumulative angular displacements
The folders "functions" and "TOOLBOX_MOVIES" contain support scripts.
DOI: 10.5281/zenodo.5568757
Citation (CITATION.cff)
# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
cff-version: 1.2.0
title: MATLAB TIRFM movie scripts
message: >-
If you use this software, please cite it using the
metadata from this file.
type: software
authors:
- given-names: Matthias
family-names: Schickinger
- given-names: Philip
family-names: Ketterer
- given-names: Jonas
family-names: Funke
- given-names: Anna-Katharina
family-names: Pumm
- given-names: Wouter
family-names: Engelen
- given-names: Eva
family-names: Bertosin