celltrackscolab-viewer

A simple plugin to visualize tracks stored in the CellTracksColab format

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CellTracksColab Viewer: Alpha Testing

Thank you for participating in the alpha testing of the CellTracksColab Viewer plugin! Please follow the steps below to install and test the plugin in Napari.

Prerequisites

Before installing the plugin, make sure you have the following set up:

1. Python 3.7 or later: You can download it from the official Python website.

2. Napari: If you don’t already have Napari installed, you can install it via pip or use Conda to manage your environment.

   To install Napari with pip:

   pip install "napari[all]"

   Alternatively, you can install it using Conda (recommended for managing Python environments):

   conda create -n napari-env python=3.9
   conda activate napari-env
   pip install napari

Step 1: Clone the Plugin Repository

1. Open a terminal or command prompt.

2. Clone the plugin repository from GitHub:

   git clone https://github.com/CellMigrationLab/celltrackscolab-viewer.git
   cd celltrackscolab-viewer

This will create a local copy of the plugin repository on your computer.

Step 2: Install the Plugin Locally

1. After cloning the repository, navigate to the plugin folder (if not already there).

2. Install the plugin in editable mode:

   pip install -e .

   The -e flag installs the plugin in "editable" mode, allowing you to make changes and test them immediately without needing to reinstall the plugin.

Step 3: Run Napari and Test the Plugin

1. Once the plugin is installed, you can start Napari by typing:

   napari

2. In Napari, go to the Plugins menu and look for CellTracksColab Viewer. From here, you can:

   • Load CSV data: Use the plugin to load track data from CSV files. Here you should open the merged_Spots.csv file
   • Load TIFF images (optional): You can load corresponding microscopy TIFF images and overlay them with track data.
   • Visualize Tracks: Select filenames and visualize the tracks in the Napari viewer.

3. test data is available here

Step 4: Reporting Bugs and Providing Feedback

If you encounter any issues or have feedback, please report them by creating an issue in the GitHub repository:

1. Go to the Issues section of the repository.
2. Create a new issue, providing as much detail as possible, including:
   • Steps to reproduce the issue.
   • Screenshots or error messages (if applicable).
   • Napari version and operating system (Windows, macOS, or Linux).

Thank you for your time and feedback!

Step 5: Installation instructions when ready

This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.

Installation

You can install celltrackscolab-viewer via pip:

pip install celltrackscolab-viewer

To install latest development version :

pip install git+https://github.com/CellMigrationLab/celltrackscolab-viewer.git

Contributing

Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.

License

Distributed under the terms of the MIT license, "celltrackscolab-viewer" is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.