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Zarr updates #16

Merged
merged 3 commits into from
Apr 2, 2024
Merged

Zarr updates #16

merged 3 commits into from
Apr 2, 2024

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akhanf
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@akhanf akhanf commented Apr 2, 2024

A few minor updates/fixes:

  1. Make the use of zipstores for final ome.zarr optional (disabled by default). The config['ome_zarr']['use_zipstore'] flag controls this now. Zipstores are not technically supported by ome-zarr (even though they work with zarr python library), so made this optional.. Made a generic rule to copy from work, so the intensive reading/writing of zarr files is still all done in localscratch if desired.. closes Make zipped outputs optional (not the default) #11
  2. ome-zarr outputs had the wrong metadata for axes, using micrometers when the values were actually millimeters. This makes the axis label millimeters as well. closes Units incorrect (mm vs um) #13
  3. removes any atlasreg rules, scripts, resources, since that is now done in SPIMquant (to be released soon) closes remove atlas registration rules #15

@akhanf akhanf merged commit cf9f3fa into main Apr 2, 2024
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@akhanf akhanf deleted the zarr-updates branch April 2, 2024 20:51
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remove atlas registration rules Units incorrect (mm vs um) Make zipped outputs optional (not the default)
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