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Allow import of 2D OME-Zarr data #6740

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normanrz opened this issue Jan 13, 2023 · 4 comments · Fixed by #7349
Closed

Allow import of 2D OME-Zarr data #6740

normanrz opened this issue Jan 13, 2023 · 4 comments · Fixed by #7349

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@normanrz
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Detailed Description

If a dataset only has 2 space dimensions, wk should be able to import it. We even have optimized ui for datasets with depth=1.

@frcroth
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frcroth commented Jul 18, 2023

Seems to be already possible. The dataset https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0083A/9822152.zarr can be imported. When opening, the XY view automatically uses the entire viewport.
When clicking on YZ or XZ wk is very confused
image
image
Perhaps these buttons should be disabled by the frontend?

@frcroth
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frcroth commented Jul 18, 2023

I tested the sample datasets from https://idr.github.io/ome-ngff-samples/ here: https://docs.google.com/spreadsheets/d/1k3ObciCJ-7AevjROgX4QP3czPluYnNK3ySzwXC6rNnw/edit?usp=sharing

Datasets worked when they were version 0.4 and had a multiscales entry (instead of plate and wells).

@normanrz
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Did you find a non-plate dataset with just XYC axes? eg https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0076A/10501752.zarr

@frcroth
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frcroth commented Sep 4, 2023

I added the remaining datasets to the sheet. The mentioned dataset has all data in dtype double, which is not supported.
To import the dataset I had to adjust axisorder things, which I did on https://github.com/scalableminds/webknossos/tree/2d-datasets, however there does not seem to be a data set to test it on

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