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

Clarifying that multiscale images can only be the same image downscaled #260

Open
LucaMarconato opened this issue Sep 4, 2024 · 0 comments

Comments

@LucaMarconato
Copy link

LucaMarconato commented Sep 4, 2024

If I am correct, the OME-NGFF specification does not require a multiscale image to be the same image downscaled. I think we should clarify and maybe enforce this for a series of reasons:

1. Different semantic

Looking at the new specs from @bogovicj, the general coordinate transformations are stored in multiscales->coordinateTransformations, while the transformations for the scales are stored in multiscales->datasets->coordinateTransformations. So it makes sense to me to keep the two transformations semantics separate, and restrict the latter to scale + translation.

2. Use in software

I would find unexpected if zooming in in napari the image/contrast limits/colors suddently change. This would occur if a multiscale image can contain images that are not downscaled. Also, having very different images in various scales could lead to algorithms giving very different results depending on the scale that is used.

3. Limitations

If using separately acquired images for different scales is allowed, then either the transformations for the multiscales are scale+translation either they are general transformations. In the first case the user would not be able to use an image as a scale in a multiscale image if the image has the slightest rotation, which would feel strange to me. In the second case, implementations (e.g. napari) would be much more complex since we can't just pass a list of images anymore.

Final comment

Common use cases would still be, of course, allowed: an user with an additional image would still be able to align it to a multiscale image via the new coordinate transformations in multiscales->coordinateTransformations.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant