Accessing the transform parameters and applying them

[nvladimus]

Hi, everyone,
Many thanks for creating this plugin, it works right out of the box on my data!
I am registering light-sheet imaged mouse brains to Allen Brain Atlas. After a 2-step registration (affine, then Bspline) I would like to take those transform parameters and apply them to the Allen Brain Atlas labels file. Is there a way to do this? Can I fetch the registration parameter files somehow from the plugin? Can I then apply them to a new stack which contains labels?
Many thanks! 🙏
Nikita

[MathieuBo]

I would be very interested in being able to do that as well!

[ntatsisk]

Hi @nvladimus and @MathieuBo, as far as I understand this is not possible at the moment. However, it sounds quite reasonable so I will take a look and try to implement it.

[ntatsisk]

I added the option to save the transform parameters with #30. I plan to add a widget for the transformix so that you can also transform the labels inside napari.

[nvladimus]

Many thanks!

[ntatsisk]

Hi @nvladimus and @MathieuBo,
FYI

• I just added the transformix widget with ENH: Add transformix widget #31 - to be released with the new version
• You can write the result images to disk by the PR ENH: Add image writer InsightSoftwareConsortium/napari-itk-io#9 in napari-itk-io plugin that gets installed together with the current plugin
• We are giving a demo about the elastix-napari plugin this week (Elastix presentation and demos, April & May 2023! elastix#868). If you happen to drop by we could discuss your use cases - that would be interesting!

Let me know if you try the changes, and also about any other feature request :)

[nvladimus]

Hi, @ntatsisk ,
Many thanks for your update! Unfortunately I dropped the image processing part to focus of imaging and optics. So I can't test the new version at the moment. But I will return to it as soon as I resume image processing, possibly in a few months. Will be happy to test your plugin, provide feedback, and maybe even contribute!

[ntatsisk]

Great! I am closing this, feel free to open a new issue if anything does not work as expected.

For a list of possible future features, you can take a look here: #35