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useful-packages-for-cell-trajectories-quantification

This repository contains several useful but small python packages which helps you to quantify the cell trajectories storaged in XML file and exported by TrackMate plugin in Fiji.

https://github.com/elephessung/useful-packages-for-cell-trajectories-quantification

Science Score: 44.0%

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    Low similarity (5.9%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

This repository contains several useful but small python packages which helps you to quantify the cell trajectories storaged in XML file and exported by TrackMate plugin in Fiji.

Basic Info
  • Host: GitHub
  • Owner: ElephesSung
  • Language: Python
  • Default Branch: main
  • Size: 51.8 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 4
Created almost 2 years ago · Last pushed almost 2 years ago
Metadata Files
Readme Citation

README.md

Useful-Packages-for-Cell-Trajectories-Quantification

This repository contains several useful but small python packages which helps you to quantify the cell trajectories storaged in XML file and exported by TrackMate plugin in Fiji.

1. TrackusRevelio

'TrackusRevelio' is a Python package designed to unravel and extract tracks from XML files exported by TrackMate in Fiji/ImageJ. This tool helps in converting the XML data into a Python list containing the instaneous speeds of the particles/cells/tracks for further analysis and processing. Please read the README.md for this package to know how to use it.

You can install it via pip: sh pip install trackus-revelio

2. velocityvortex

velocityvortex is a Python package for calculating the Velocity Autocorrelation Function (VAF) from XML files exported by TrackMate in Fiji/ImageJ. This tool converts tracking data into velocity vectors and computes their autocorrelation over time, helping analyze cell trajectories and dynamics. Please read the README.md for this package to know how to use it.

You can install it via pip: sh pip install velocityvortex

Owner

  • Name: Fan-Hsin Sung
  • Login: ElephesSung
  • Kind: user
  • Location: London
  • Company: Imperial College London

Citation (CITATION.cff) 

cff-version: 0.1.5
message: "If you use this software, please cite it as below."
authors:
- family-names: Sung
  given-names: Elephes
orcid: https://orcid.org/0000-0003-2091-542X
title:Useful Packages for Cell Trajectories Quantification: TrackusRevelio 0.1.5
version: 0.1.5
date-released: 2024-07-24

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Dependencies

VelocityVortex/pyproject.toml pypi
  • numpy >=1.26.0
  • python ^3.8
trackus-revelio/pyproject.toml pypi
  • numpy >=1.26.0
  • python ^3.7