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We want to compute statistics from the FOV-scale zarr store and store it with patch-scale zarr store, which dataloader will parse.
The process for this is:
Compute statistics per FOV (not patch) and store these with metadata.
Normalize using FOV statistics at training and test time - use existing CLI or preprocessing script.
This is current structure of the patches ome_zarr:
=== Summary ===
Format: omezarr v0.4
Axes: T (time); C (channel); Z (space); Y (space); X (space);
Channel names: ['RFP', 'Phase3D']
Row names: ['A', 'B']
Column names: ['3', '4']
Wells: 4
Positions: 2629
This is structure of track_labels zarr where we can store the meta data: (fov information can be stored here)
=== Summary ===
Format: omezarr v0.4
Axes: T (time); C (channel); Z (space); Y (space); X (space);
Channel names: ['tracking']
Row names: ['A', 'B']
Column names: ['3', '4']
Wells: 4
Positions: 61
Need help on how to integrate metadata into the track ome_zarr, how this will be used to generate the patch ome_zarr and then eventually the dataloader for normalization.
The text was updated successfully, but these errors were encountered:
Need help on how to integrate metadata into the track ome_zarr, how this will be used to generate the patch ome_zarr and then eventually the dataloader for normalization.
We want to compute statistics from the FOV-scale zarr store and store it with patch-scale zarr store, which dataloader will parse.
The process for this is:
This is current structure of the patches ome_zarr:
=== Summary ===
Format: omezarr v0.4
Axes: T (time); C (channel); Z (space); Y (space); X (space);
Channel names: ['RFP', 'Phase3D']
Row names: ['A', 'B']
Column names: ['3', '4']
Wells: 4
Positions: 2629
This is structure of track_labels zarr where we can store the meta data: (fov information can be stored here)
=== Summary ===
Format: omezarr v0.4
Axes: T (time); C (channel); Z (space); Y (space); X (space);
Channel names: ['tracking']
Row names: ['A', 'B']
Column names: ['3', '4']
Wells: 4
Positions: 61
Need help on how to integrate metadata into the track ome_zarr, how this will be used to generate the patch ome_zarr and then eventually the dataloader for normalization.
The text was updated successfully, but these errors were encountered: