Adaptive Pixel Reassignment

It performs Adaptive Pixel Reassignment via a phase-correlation algorithm. Once installed, you can upload any ISM-dataset in .h5 or .npy format. The plugin expects a numpy array of the format rzxytc (r: repetition, z: axial dimension, xy: lateral dimensions, t: time dimension, c: detector element). If the rzt dimensions are not present, add manually fake dimensions (e.g. using the numpy.expand_dims function). You can also generate a synthetic ISM-dataset from the File menu. Once a dataset is uploaded on an image layer, you can use the Napari plugin menu to perform either a sum on the c dimension or perform Adaptive Pixel Reassignment on the c dimension.

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Installation¶

You can install napari-ISM via pip:

pip install napari-ISM

It requires the following Python packages

numpy
scipy
scikit-image
h5py
napari

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 GNU LGPL v3.0 license, "napari-ISM" is free and open source software

Issues¶

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