Robust image registration for napari
Project description
napari-pystackreg
Robust image registration for napari.
Summary
napari-pystackreg offers the image registration capabilities of the python package pystackreg for napari.
Description
pyStackReg is used to align (register) one or more images to a common reference image, as is required usually in
time-resolved fluorescence or wide-field microscopy.
It is directly ported from the source code of the ImageJ plugin TurboReg
and provides additionally the
functionality of the ImageJ plugin StackReg
, both of which were written by Philippe Thevenaz/EPFL
(available at http://bigwww.epfl.ch/thevenaz/turboreg/).
pyStackReg provides the following five types of distortion:
- translation
- rigid body (translation + rotation)
- scaled rotation (translation + rotation + scaling)
- affine (translation + rotation + scaling + shearing)
- bilinear (non-linear transformation; does not preserve straight lines)
pyStackReg supports the full functionality of StackReg plus some additional options, e.g., using different reference images and having access to the actual transformation matrices (please see the examples below). Note that pyStackReg uses the high quality (i.e. high accuracy) mode of TurboReg that uses cubic spline interpolation for transformation.
Please note: The bilinear transformation cannot be propagated, as a combination of bilinear transformations does not generally result in a bilinear transformation. Therefore, stack registration/transform functions won't work with bilinear transformation when using "previous" image as reference image. You can either use another reference ( "first" or "mean" for first or mean image, respectively), or try to register/transform each image of the stack separately to its respective previous image (and use the already transformed previous image as reference for the next image).
This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.
Installation
You can install napari-pystackreg
via pip:
pip install napari-pystackreg
To install latest development version :
pip install git+https://github.com/glichtner/napari-pystackreg.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 Apache Software License 2.0 license, "napari-pystackreg" is free and open source software
Issues
If you encounter any problems, please file an issue along with a detailed description.
Project details
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