---
# System prepended metadata

title: IDR-NGFF 2021-W01+02
tags: [NGFF]

---

---
tags: NGFF
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# IDR-NGFF 2021-W01+02

## 2021-01-11

* Will:
  - received word from Trevor. Need time to look at it.
  - started looking into 3d-sampling, but nothing to show yet.
* Josh:
  - no word from https://github.com/Kitware/itk-vtk-viewer/issues/315
  - for discussion on Tuesday: likely to ramp up more on the light sheet front after prod92 in time for the end of July trainings, then can go back to prod93

## 2021-01-06

* "lightsheet" epic:
  - Goal: have one or more (idr0101, idr0044, etc.) large 3D volumes converted and usable.
  - Minimal spec changes: voxel size, scale information in Zarr
  - Main issue: Sub-resolutions in Z, chunking in Z
    - Multiple chunkings versus fixing subresolutions in Z?
    - Re-using the base resolution?
    - Simon: downsampling T? Seb: seen no downsampling need
  - 3D client(s)?
    - [Kitware example](https://kitware.github.io/itk-vtk-viewer/app/?fileToLoad=https://thewtex.github.io/allen-ccf-itk-vtk-zarr/average_template_50_chunked.zarr)
       - J-M: I tried it at the end of last year with our example from S3, it did not load, either S3 issue or our zarr file.
       - https://github.com/Kitware/itk-vtk-viewer/pull/343
       - https://github.com/Kitware/itk-vtk-viewer/issues/315
       - https://github.com/Kitware/itk-vtk-viewer/issues/176
    - MoBIE / BDV? (ome-zarr-java?) - demo Jan 29th.
    - Others
      - napari - open PRs to make 3D work?
        - https://github.com/napari/napari/pull/323
      - neuroglancer
      - viv (2D)
      - fpbioimage
  - Performance
    - Nested zarrs (ZarrV3?, consolidated?)
    - ZarrReader & native s3 imports (for converted data)
    - Import original (e.g. BDV, KLB, IMS), OME-TIFF, and OME-Zarr and compare performance. eg idr0101 data
 * AOB
   - J-m: zarr_implementations repo is failing. See one open PR.
     - download from S3 using Rust faster than go.
   - Will: looking at Vitesse for displaying OME-Zarr data
     - They contributed some fixes. Not using rendering settings. (Not setup to do that)
     - Discussion about their multiple repositories.
     - Do we focus on ome-zarr-js and ome-zarr-java?