Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Using "register_function" to add custom workflows #17

Open
3 tasks
pr4deepr opened this issue Sep 27, 2022 · 3 comments
Open
3 tasks

Using "register_function" to add custom workflows #17

pr4deepr opened this issue Sep 27, 2022 · 3 comments
Labels
enhancement New feature or request help wanted Extra attention is needed

Comments

@pr4deepr
Copy link
Collaborator

@haesleinhuepf showed us how we can add functions using
@register_function
juglab/napari-n2v#6 (comment)
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:

  • Cellpose
  • ilastik
  • regionprops measurements table?
@pr4deepr pr4deepr added enhancement New feature or request good first issue Good for newcomers help wanted Extra attention is needed and removed good first issue Good for newcomers labels Sep 27, 2022
@haesleinhuepf
Copy link
Contributor

  • 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
Copy link
Collaborator Author

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
Copy link
Contributor

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? 🙃

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request help wanted Extra attention is needed
Projects
None yet
Development

No branches or pull requests

2 participants