napari-J

A plugin to exchange data with FIJI and to use FIJI image analysis from napari. Current features are:

• get the active image from FIJI
• send a screenshot to FIJI
• get a set of points from the FIJI results table
• filter the points in napari
• send the filtered points back to FIJI

Known problems:

• Crashes on linux when the file-dialog is opened. Workaround: Set the option Use JFileChooser to open/save from the Edit>Options>Input/Output menu.
• 03.05.2022 - Currently you need to have the range of the quality values for point between 0 and 255, in the new version they can have any range, but we are waiting for the bug in napari 0.4.15 to be fixed to release this.

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This napari plugin was generated with Cookiecutter using with @napari's cookiecutter-napari-plugin template.

Installation¶

You can install napari-J via pip:

pip install napari-J

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 MIT license, "napari-J" is free and open source software

Issues¶

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