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

Convert PS-OCT MAT files to OME-Zarr #19

Merged
merged 55 commits into from
Nov 21, 2024
Merged

Convert PS-OCT MAT files to OME-Zarr #19

merged 55 commits into from
Nov 21, 2024

Conversation

calvinchai
Copy link
Contributor

No description provided.

@calvinchai calvinchai marked this pull request as ready for review November 19, 2024 15:59
@calvinchai
Copy link
Contributor Author

Refactor the pyramid part is done. More need to be refactored will be done when I work on other modalities. Now it also lazy loads the files instead of loading all at once.

@kabilar kabilar changed the title oct_mat_to_zarr Convert PS-OCT MAT file to Zarr Nov 19, 2024
@kabilar kabilar changed the title Convert PS-OCT MAT file to Zarr Convert PS-OCT MAT files to OME-Zarr Nov 19, 2024
@balbasty
Copy link
Collaborator

I went (very very) quickly thourgh it and it looks fine.

The only question I have, and I think we'll have to check with Nate, is how the channels of the input file map to its spatial axes. Say differently, each voxel contains an orientation vector and we need to understnad in what referential this orientation vector is. In the output zarr, we'll want the first channel to correspond to dimension "x", the second channel to dimension "y", etc.

@calvinchai
Copy link
Contributor Author

Probably we can revisit that later? We can open an issue and merge this first.

I went (very very) quickly thourgh it and it looks fine.

The only question I have, and I think we'll have to check with Nate, is how the channels of the input file map to its spatial axes. Say differently, each voxel contains an orientation vector and we need to understnad in what referential this orientation vector is. In the output zarr, we'll want the first channel to correspond to dimension "x", the second channel to dimension "y", etc.

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

Successfully merging this pull request may close these issues.

3 participants