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feat: add ND2 reader and OME-Zarr converter - #436
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Wrap nd2.ND2File as an iohub reader (ND2Dataset/ND2FOV) and route .nd2 paths through read_images and TIFFConverter. Each stage position maps to one FOV; data is returned in canonical TCZYX with native dtype preserved (no downcast, no axis swaps). Supports OME-NGFF v0.4 and v0.5. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
nd2.to_xarray returns axes in native, non-canonical order (e.g. Z before C for multichannel z-stacks). The round-trip comparison now transposes the expected array to canonical TCZYX by label instead of assuming order, so it holds for any axis combination rather than only single-non-singleton-axis files. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
srivarra
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Jul 7, 2026
Add Nikon ND2 to the README supported-formats list (and Osprey to the Biohub microscopes line), and document ND2Dataset/ND2FOV in the reader API reference. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Regenerate uv.lock after adding nd2 to pyproject; pulls in nd2 and its transitives (ome-types, xsdata, resource-backed-dask-array). No changes to existing pins. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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@jenniferdoherty6 I've tested this on the datasets you've provided, and it seems to work. Let me know how it goes for you. |
ieivanov
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Jul 14, 2026
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Took a quick look, looks good I think
Signed-off-by: Sricharan Reddy Varra <sricharan.varra@biohub.org>
Signed-off-by: Sricharan Reddy Varra <sricharan.varra@biohub.org>
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Adds support for nd2 / osprey.
Todos:
Will do some housekeeping after to generalize the MicroManagerFOV + MicroManagerFOVMapping class in a separate pr.