crop in transformed coordinates

[martinschorb]

Hi,

I like to crop a dataset in an arbitrary orientation.

However, the bounding box is only shown in the original volume coordinates. Can I provide a transformed source and crop it in the viewer's frame?

[tischi]

Yes, you can using: [Process > Transform] (enter an affine transform) and then afterwards do [Process > Crop...]. Would that work for you?

[tischi]

I can also try to make the Manual Transform [T] work (which currently does not); would that help?

[martinschorb]

My actual intention was to use the cropping to define sources for a gallery view of subvolumes. mobie/mobie.github.io#32
I am trying to find out how the cropping and transformation could be best stored in a MoBIE2 compatible way.

[martinschorb]

so it seems there is no way of storing a crop only in metadata. Even when I load a BDV/XML dataset into BDP2 and crop it saving requires to write a new data container. Would it be possible to do this entirely at the metadata level? So that instead of defining transformations only, I could also define the crop bounding box? Ideally in the same logic of a transformation... So one could even do:

transformation -> crop (arbitrary BBox orientation) -> transform (display)

[tischi]

Conceptually possible.

@NicoKiaru do we have a crop( SourceAndConverter sac, Interval interval ) in the playground?

@constantinpape @K-Meech do you feel having a spec for a crop of an image in MoBIE would be something generally useful (to me it feels that could be something useful in order show sub-volumes of big image data sets)

@martinschorb regarding "arbitrary BBox orientation" I think the easiest would be to first transform the source into a space where you can then crop along the cartesian axes (and the crop would be given in this coordinate system).

[martinschorb]

I think the easiest would be to first transform the source into a space where you can then crop along the cartesian axes (and the crop would be given in this coordinate system).

Yes, that's precisely what I thought of and what I would need in that gallery use case.

[constantinpape]

@constantinpape @K-Meech do you feel having a spec for a crop of an image in MoBIE would be something generally useful (to me it feels that could be something useful in order show sub-volumes of big image data sets)

Yes, I agree that could be useful, as already discussed in mobie/mobie.github.io#32.
I have made an issue in the mobie repo on this mobie/mobie.github.io#44.

[tischi]

@martinschorb Would you already have a convenient workflow for how to determine the transformation and crop? Or should we add something to BDV-Playground or BigDataProcessor2?

[martinschorb]

Would you already have a convenient workflow for how to determine the transformation and crop

Yes, that is all ready to go. The scenario is:

• volume that includes a centriole
• I transform such that the major axis of the centriole is in the center of the FOV and parallel to x.
• now I want to only show a gallery of many centrioles in that orientation
• this means I need to crop the individual sources to the subvolume around the centrioles
• so the BBox would be center +- xyz in physical coordinates after applying this targeting transformation