Dataset layout and metadata¶
Acquisition and image axes¶
The supported input is a current qi2lab opm-v2 filesystem-backed OME-Zarr acquisition. Its manifest and OME/NGFF metadata provide calibration, channels, stage positions, and scan geometry.
| Representation | Axes | Meaning |
|---|---|---|
| Logical acquisition view | TPCZYX | Time, position, channel, scan plane, camera Y, camera X |
| Per-position image array | TCZYX | One positioned image series |
| Deskewed tile | TCZYX | Laboratory Z replaces the raw scan-plane axis |
| Fused image | TCZYX | Registered laboratory coordinates |
| Maximum-Z image | TCZYX | Z has length one |
Position collections retain separate positioned arrays and their transforms. The OME-Zarr image metadata defines physical scales and translations; positions in the acquisition description may use ZXY or XYZ ordering as named by their fields. Do not interpret the raw scan-plane dimension as laboratory Z.
Output files¶
<stem> is the acquisition name. Files default to the acquisition directory,
or to the directory supplied with process --output.
| Output | Contents |
|---|---|
<stem>_deskewed.ome.zarr |
Calibrated, deskewed position collection |
<stem>_decon_deskewed.ome.zarr |
Deconvolved, deskewed position collection |
<stem>_max_z_deskewed.ome.zarr |
Per-tile maximum-Z images |
<stem>_max_z_decon_deskewed.ome.zarr |
Per-tile deconvolved maximum-Z images |
<stem>_fused.ome.zarr |
Registered fused multiscale image |
<stem>_max_z_fused.ome.zarr |
Registered fused maximum-Z multiscale image |
<stem>_flatfield.ome.tif |
Estimated illumination fields, when requested |
<stem>.processing.json |
Processing configuration, completion, source path, and registration state |
<stem>_depth_intensity_gains.json |
Fitted gains and depth-normalization provenance |
<stem>_roi.json |
Saved physical ROI selection |
<stem>_roi/ |
Default ROI processing destination |
Native planar acquisitions use their planar output naming convention. Inspect the command's printed destination and journal to identify its output stores.
Processing journal¶
One journal describes the source and outputs for an acquisition. Image stores contain OME/NGFF image metadata; mutable processing checkpoints are kept in the journal. Run fingerprints include the settings and geometry needed for compatible resume. Completion is recorded after writes are durable.
The journal also locates the raw acquisition when ROI processing or export is launched from a separate output directory. Keep that raw path accessible, and keep the journal beside the outputs when moving a dataset.
Units and pyramids¶
Spatial transforms use micrometers. Time axes retain the units recorded in the metadata. Command ranges are zero-based and stop-exclusive; registration shift and blending options use processed-image pixels in ZYX order.
The fused OME-Zarr volume has reduced spatial levels. Its maximum-Z image is generated from each registered fused level. OME-TIFF export currently writes only level zero and preserves a singleton Z axis for the projection. OME-XML stores channel metadata, physical units, and plane positions, with provenance annotations when the journal and acquisition are available.
See acquisition and state functions for the corresponding Python structures.