napari-EMD

A simple plugin to view .emd files in napari (i.e. Velox files). Allows users to track metadata as it changes over the course of a video/stack, developed for analysis of in-situ microscopy data, where users may be changing magnification, focus, etc. during aquisition.

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

Installation

You can install napari-EMD via pip:

`pip install napari-EMD`

You can install napari and access the plugin through the GUI. Reccomended install command for napari:

`python -m pip install "napari[all]"`

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-EMD" is free and open source software

Issues and Requests

Warning: The metadata viewer does not work in the current Napari bundle version (August 2023). Use the python package version of Napari for this feature.

If you encounter any problems or would like any functionality added, please file an issue along with a detailed description.

Current maintainer(s): Nicki Shaw

Preview

Images A and B show different frames in the same image stack, the metadata plugin on the right shows the changing focus value.

To Do

• Attatch last-opened information, so the widget does not reset when frames are changed and open toggle options are open remain.
• Add a search bar for navigating metadata.
• Output metadata as file option.
• Add note to change order of open files to replacee active metadata view.
• Make Singleframe note update automatically on change of file order.