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mint

Modified Intraneuronal Nanoparticle Tracking (MINT) is a Python script used to extract intraneuronal transport parameters from the trajectories of optically active nanoparticles.

https://github.com/biophotlumin/mint

Science Score: 67.0%

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    Found 3 DOI reference(s) in README
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    Low similarity (6.7%) to scientific vocabulary

Keywords

nanoparticle neuroscience tracking
Last synced: 6 months ago · JSON representation ·

Repository

Modified Intraneuronal Nanoparticle Tracking (MINT) is a Python script used to extract intraneuronal transport parameters from the trajectories of optically active nanoparticles.

Basic Info
Statistics
  • Stars: 2
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 8
Topics
nanoparticle neuroscience tracking
Created over 4 years ago · Last pushed about 1 year ago
Metadata Files
Readme License Citation

README.md

MINT

Modified Intraneuronal Nanoparticle Tracking (MINT) is a Python script used to extract intraneuronal transport parameters from trajectories of optically active nanoparticles.

It relies on trackpy to extract trajectories from videos, from which transport parameters are then calculated and statistically tested.

It can reasonably be applied to videos of fluorophore-labelled organelles or similar experiments.

Please refer to the documentation for further information.

Quickstart

Install the latest version : 

git clone https://github.com/biophotlumin/mint.git

cd mint

pip install .

You can then run MINT with :

mint -f <input_folder> -p <path/to/file> -l -e -s

-f, --folder : Path to raw data folder.

-p, --params : Path to config file (YAML or JSON).

-l, --locate : Run tracking.

-e, --extract : Extract transport parameters from trajectories.

-s, --stats : Run statistical analysis.

Owner

  • Name: LuMIn Biophotonique
  • Login: biophotlumin
  • Kind: organization

# All our materials related to the tracking device

Citation (CITATION.cff) 

cff-version: 1.1.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: Grimaud
    given-names: Baptiste
title: mint
version: v0.2.0
date-released: 2023-03-02

GitHub Events

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  • Delete event: 2
  • Push event: 1

Dependencies

requirements.txt pypi
  • PyInquirer ==1.0.3
  • PySimpleGUI ==4.57.0
  • cvxpy ==1.1.7
  • imageio ==2.9.0
  • matplotlib ==3.5.0
  • numpy ==1.21.2
  • opencv_python ==4.5.3.56
  • pandas ==1.3.5
  • prompt_toolkit ==1.0.14
  • scikit_posthocs ==0.6.7
  • scipy ==1.5.3
  • seaborn ==0.11.2
  • trackpy ==0.5.0
docs/requirements.txt pypi
  • PyYAML ==6.0
  • cvxpy ==1.3.0
  • fpdf2 ==2.6.1
  • imageio ==2.23.0
  • matplotlib ==3.5.3
  • nd2 ==0.5.3
  • numba ==0.56.4
  • numpy ==1.21.5
  • opencv_python ==4.7.0.68
  • pandas ==1.3.5
  • pydata-sphinx-theme ==0.13.0
  • scikit_posthocs ==0.7.0
  • scipy ==1.7.3
  • scs ==3.2.2
  • seaborn ==0.12.2
  • sphinx ==5.3.0
  • trackpy ==0.6.1