A plugin to load images stored in MATLAB .mat files with napari
This plugin loads image variables stored in
.mat files into napari.
It loads any variable that looks like an image.
Presently, that includes any array with more than two dimensions with size greater than 20 pixels (determined by
If loading a variable with 3 or more dimensions, the plugin assumes that it is a stack of images, and the dimension with greatest size is the axis of the stack.
Loading Large Files
If loading a large
.mat file saved in
v7.3 format, chunks of the images are loaded as needed, resulting in fast initial load, but potentially slower scrolling.
Slices of the image stacks are randomly sampled to determine min/max contrast values.
This plugin relies on
scipy to load small
.mat files and
dask) to load larger
It implicitly requires
napari for use.
napari-mat-images requires napari to be installed, although it is not listed as a requirement for installation.
This plugin relies on plugin functionality found in
napari version >
0.2.12. This can be installed via pip from PyPI:
$ pip install napari>0.2.12
$ pip install napari-mat-images
Once installed, the plugin will be used whenever trying to load a
This can be done from the
napari GUI or commandline:
$ napari my_file.mat
Contributions are very welcome. Tests can be run with pytest, please ensure the coverage at least stays the same before you submit a pull request.
Distributed under the terms of the BSD-3 license,
napari-mat-images is free and open source software
If you encounter any problems, please file an issue along with a detailed description.
- 30 June 2021
- 29 March 2020
- 4 - Beta
- Stars: 1
- Forks: 1
- Issues + PRs: 2
Python versions supported:
- OS Independent