A napari plugin to define subboxing transformations and a CLI tool to apply them.

The plugin is under active development, unstable and provided with no guarantees. If you would like to use it and require help, please get in touch!

You can install napari-subboxer via pip:

pip install napari-subboxer

It is recommended to install napari-subboxer into a clean virtual environment.

The expected workflow for using this plugin and further refinement is

1. define and save subboxing transformations using napari-subboxer define
2. apply transformations using napari-subboxer apply
3. re-reconstruct/extract your particle set with the new set of poses
4. reconstruct your particles to create a new reference centered on your subparticle
5. refine refine refine!

napari-subboxer define define has three modes, activated via buttons in the GUI

• add new point
• define z-axis of each point
• define in plane orientation of each point

In add or define-z mode alt-click on the plane to add a new point. In in-plane mode alt-click and drag to set the in plane orientation of the current point

The plane can be moved by clicking and dragging. The plane can be reoriented with the x/y/z/o keys (o sets the plane normal to the camera view direction).

Subboxing transformations can currently only be applied on RELION 3.1 star files.

Contributions are very welcome.

Distributed under the terms of the BSD-3 license, "napari-subboxer" is free and open source software

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