Napari Correct Drift
Drift correction 2D/3D for Napari similar to Fijis Correct 3D drift macro
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
https://user-images.githubusercontent.com/895863/235100349-83379350-06a5-4fe7-9323-f3e5771cca2e.mp4
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
- [x] Basic CorrectDrift interface
- [x] Synthetic test data
- [x] Unit tests
- [x] 2D/3D multi-channel support
- [x] ROI support (rectangles)
- [x] Saving and loading of drift tables
- [x] Outlier handling
- [x] Sphinx documentation
- [x] How-tos
- [x] 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:
- 2023-11-06
First released:
- 2023-04-26
License:
- BSD-3-Clause
Supported data:
- Information not submitted
Plugin type:
Open extension:
Save extension:
Operating system:
- Information not submitted
Requirements:
- napari
- numpy
- qtpy
- pandas
- scikit-image
- scipy
- dask
- tox ; extra == 'testing'
- pytest ; extra == 'testing'
- pytest-cov ; extra == 'testing'
- pytest-qt ; extra == 'testing'
- napari ; extra == 'testing'
- pyqt5 ; extra == 'testing'