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

OME-ZARR support for BigStitcher-Spark #40

Merged
merged 42 commits into from
Feb 5, 2025
Merged

OME-ZARR support for BigStitcher-Spark #40

merged 42 commits into from
Feb 5, 2025

Conversation

StephanPreibisch
Copy link
Contributor

Full OME-ZARR support for export of fused volumes (except for non-rigid fusion), also now uses the fusion code from multiview-reconstruction.

Documentation is not fully done, merging now so Tobias can work on it ...

@tpietzsch @krokicki @takashi310 @mkitti

Copy link
Contributor

@mkitti mkitti left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I'm curious about how much of the OME part is actually implemented here as opposed to just Zarr.

@mkitti
Copy link
Contributor

mkitti commented Feb 5, 2025

Os the OME version declared anywhere?

{
  ...
  "attributes": {
    "ome": {
      "version": "0.5",
      ...
    }
  }
}

@StephanPreibisch StephanPreibisch merged commit cacf0d1 into main Feb 5, 2025
1 check passed
@StephanPreibisch
Copy link
Contributor Author

StephanPreibisch commented Feb 5, 2025

This is using the implementation of @bogovicj ... so it is fully implemented (except for the multi-well stuff etc). The exported volumes were tested in Fiji, Neuroglancer, Allen 3D Viewer, and the OME-NGFF validator.

This is the code that calls John's code: https://github.com/PreibischLab/multiview-reconstruction/blob/c2aa04fa9d9d562d053b1c76eb5ffcb3a9f74af9/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/OMEZarrAttibutes.java#L54-L131

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.

2 participants