napatrackmater

napatrackmater

Import Trackmate XML files for Track Visualization and analysis in Napari.

Napari Visualization tool for Trackmate > 6.0 and bTrackmate XML files for 3D + time tracks.

This repository is the bridge between the Fiji and Napari world for exporting and viewing the track XML files using Napari track layer.

Build Status PyPI version

Installation

This package can be installed with:

pip install --user napatrackmater

If you are building this from the source, clone the repository and install via

git clone https://github.com/kapoorlab/NapaTrackMater/

cd NapaTrackMater

pip install --user -e .

# or, to install in editable mode AND grab all of the developer tools
# (this is required if you want to contribute code back to NapaTrackMater)
pip install --user -r requirements.txt

Pipenv install

Pipenv allows you to install dependencies in a virtual environment.

# install pipenv if you don't already have it installed
pip install --user pipenv

# clone the repository and sync the dependencies
git clone https://github.com/kapoorlab/NapaTrackMater/
cd NapaTrackMater
pipenv sync

# make the current package available
pipenv run python setup.py develop

# you can run the example notebooks by starting the jupyter notebook inside the virtual env
pipenv run jupyter notebook

Docker

A Docker image can be used to run the code in a container. Once inside the project's directory, build the image with:

docker build -t kapoorlab/NapaTrackMater .

Now to run the track command:

# show help
docker run --rm -it kapoorlab/NapaTrackMater
# run it with example data
docker run --rm -it -v $(pwd)/examples/data:/input kapoorlab/NapaTrackMater track -f /input -r /input/Raw.tif -s /input/Seg.tif -s /input/Mask.tif -n test

Requirements

  • Python 3.9 and above.

License

Under MIT license. See LICENSE.

Authors

Version:

  • 4.2.1

Last updated:

  • 11 September 2023

First released:

  • 16 January 2021

License:

  • BSD-3-Clause

Supported data:

  • Information not submitted

Plugin type:

  • Information not submitted

GitHub activity:

  • Stars: 17
  • Forks: 4
  • Issues + PRs: 4

Python versions supported:

Operating system:

Requirements:

  • lxml
  • vollseg
  • napari
  • natsort
  • seaborn
  • cellshape-cloud
  • cellshape-helper
  • kapoorlabs-lightning
  • lightning

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