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Napari Correct Drift

napari-correct-drift

Drift correction 2D/3D for Napari similar to Fijis Correct 3D drift macro

License BSD-3 PyPI Python Version tests codecov napari hub Documentation Status

Napari-correct-drift brings the functionality of Fiji’s popular Correct-3D-drift macro to Napari for flexible and efficient correction of stage and sample drift common in time-lapse microscopy.

Napari-correct-drift supports drift correction for 2D/3D multi-channel data.


Example

Test data

Napari-correct-drift contains synthetic sample data. To test it on real data download an example Arabidopsis growing root tip file.

Installation

You can install napari-correct-drift via [pip]:

pip install napari-correct-drift

To install latest development version :

pip install git+https://github.com/sommerc/napari-correct-drift.git

Roadmap

  • Basic CorrectDrift interface
  • Synthetic test data
  • Unit tests
  • 2D/3D multi-channel support
  • ROI support (rectangles)
  • Saving and loading of drift tables
  • Outlier handling
  • Sphinx documentation
  • How-tos
  • Tutorials and Guides

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 [BSD-3] license, "napari-correct-drift" is free and open source software

Acknowledgment

This project has been made possible in part by grant number NP2-0000000051 from the napari Plugin Foundations Grants (Cycle 2).

Version:

  • 0.4.0

Last updated:

  • 06 November 2023

First released:

  • 26 April 2023

License:

Supported data:

  • Information not submitted

Plugin type:

GitHub activity:

  • Stars: 3
  • Forks: 1
  • Issues + PRs: 0

Python versions supported:

Operating system:

Requirements:

  • napari
  • numpy
  • qtpy
  • pandas
  • scikit-image
  • scipy
  • dask

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