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feat: read Bioformats2raw#414

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srivarra merged 2 commits into
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ngff/bioformats2raw-read
May 5, 2026
Merged

feat: read Bioformats2raw#414
srivarra merged 2 commits into
mainfrom
ngff/bioformats2raw-read

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@srivarra srivarra commented May 5, 2026

You can open a bf2raw Zarr like it's a HCS plate:

from iohub.ngff import open_ome_zarr

bf2raw_data = "/hpc/instruments/cm.automaton/livescreen/2026_04_30_proj_ang_len_sweep/argolight_bullseye/pa_10_pl_2_20260430_192137/data.ome.zarr"

with open_ome_zarr(bf2raw_data) as dataset:
    print(f"{len(dataset)} series, channels: {dataset.channel_names}")
    for name, pos in dataset.positions():
        arr = pos["0"]
        print(name, arr.shape, arr.dtype)

iohub info -v <path to bf2raw.ome.zarr> also works and lists out the positions.

Signed-off-by: Sricharan Reddy Varra <sricharan.varra@biohub.org>
@srivarra srivarra linked an issue May 5, 2026 that may be closed by this pull request
…positions

Signed-off-by: Sricharan Reddy Varra <sricharan.varra@biohub.org>
@srivarra srivarra marked this pull request as ready for review May 5, 2026 19:53
@srivarra srivarra requested review from ieivanov and talonchandler May 5, 2026 19:53
@srivarra srivarra merged commit 83bbf74 into main May 5, 2026
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iohub should support reading bioformats2raw layout

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