search

BioimageAnalysisCoreWEHI / napari_lattice

Napari plugin for custom analysis and visualization of lattice lightsheet and Oblique Plane Microscopy data. The plugin is optimized for data from the Zeiss lattice lightsheet microscope.
https://github.com/BioimageAnalysisCoreWEHI/napari_lattice/wiki
GNU General Public License v3.0
12 stars 4 forks source link

Using "register_function" to add custom workflows #17

Open pr4deepr opened 2 years ago

pr4deepr commented 2 years ago

@haesleinhuepf showed us how we can add functions using @register_function https://github.com/juglab/napari-n2v/issues/6#issuecomment-1258861660 https://github.com/clEsperanto/napari_pyclesperanto_assistant/blob/ad72ecae7d017ba63f579f05dd00be627f36e89b/napari_pyclesperanto_assistant/_napari_cle_functions.py#L7

This will enable the addition of interactive workflows. Add options for popular algorithms or workflows not available in pyclesperanto-assistant:

haesleinhuepf commented 2 years ago
  • regionprops measurements table?

I recently started using infrastructure from morphometrics (by @kevinyamauchi) for this, e.g. here: https://github.com/haesleinhuepf/napari-skimage-regionprops/blob/bda457cb30d15c057669e3cd847ab5e795c4b75d/napari_skimage_regionprops/_regionprops.py#L204

pr4deepr commented 2 years ago

Ahh, this is interesting. So, you can pass a measurement function, intensity image, label image and parameters for the function.. Assuming its agnostic to the measurement function?

Do you then display the table using add_table?

haesleinhuepf commented 2 years ago

Morphometrics collects measurement functions and I presume you can ask morphometrics to apply them all to specific data. It works via the GUI. Maybe @kevinyamauchi can tell us to if/how it also works programmatically? 🙃