Himena

Pipeline between napari and himena.

napari is a great tool for visualization, annotation and analysis of multi-dimensional images. On the other hand, himena has a powerful plugin system that allows users to technically do anything, such as editing table and plotting.

napari-himena connects these two ecosystems together, enabling users to send data back and forth, extending the functionality of the both packages.

Examples¶

1. Sending image layers to himena for ImageJ-like multi-measurement and Excel-like plotting.¶

Measuring time-course change in the image intensity with himena-image plugin, and plot the result using the built-in plot functions using matplotlib.

2. Sending points and their features to himena for seaborn plotting.¶

Feature dataframe can be directly sent to himena for seaborn plotting using himena-seaborn plugin.

Usage¶

Starting from napari¶

Open the napari-himena dock widget from the "Plugin" menu, connect to one of the himena profile (only "default" is available by default), and that's it!

Starting from himena¶

To use this plugin from himena, you need to first register this plugin to the himena profile

# install to the default profile
himena --install napari-himena

# or install to a specific profile
himena <my-profile> --install napari-himena

Then all the commands will be available in himena and a napari viewer will be launched when it is needed. You don't need to do this if you always launch himena from napari plugin; it automatically register this package in the beginning.

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This napari plugin was generated with copier using the napari-plugin-template.

Installation¶

You can install napari-himena via pip:

pip install napari-himena

To install latest development version :

pip install git+https://github.com/hanjinliu/napari-himena.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 BSD-3 license, "napari-himena" is free and open source software

Issues¶

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