Map AnnData observation rows to OME-Zarr fields of view and crops.
Image views need two inputs: a mounted OME-Zarr HCS plate and observation columns that identify an image and crop location.
Associate each dataset with an HCS store in Project YAML:
datasets:
experiment_a:
anndata: ./analysis/anndata.zarr
hcs_plate: ./images/experiment-a.zarrThe value in each observation's field-of-view column is appended below that plate root. It must therefore match the image path inside the plate, for example A/1/000000.
| Purpose | Accepted names, in priority order | Required for crops |
|---|---|---|
| field of view | fov_name, then well | yes |
| time point | t | no; defaults according to the image request |
| bounding box | bbox, then cp_bbox | use this or X/Y |
| X coordinate | x, x_cp1, x_global_pheno | use with matching Y |
| Y coordinate | y, y_cp1, y_global_pheno | use with matching X |
| Z plane | z, z_slice, plane | no |
X and Y names are selected as pairs; do not mix candidates from different rows of the table.
A bounding box is a string in source-image pixel coordinates:
[y_min x_min y_max x_max]Malformed boxes are ignored. When a box is absent, the viewer centres a crop on X/Y. Keep coordinates in the full-resolution image's pixel coordinate system.
fov_name | t | z | x | y | bbox |
|---|---|---|---|---|---|
A/1/000000 | 25 | 0 | 623 | 84 | [52 591 116 655] |
The focused table row publishes this information to the Image Viewer and Gallery. A selection or filter can publish many rows for crop loading.
The mounted plate should expose a standard plate → well → image hierarchy. Image groups need multiscales; omero.channels supplies channel labels, colours, and display windows. Coordinate transformation scales provide physical X/Y spacing. Project YAML channel settings can override the initial colour, contrast, and visibility.
fov_name and verify that the same relative image path exists below the plate root./plate or /plate/<dataset>.A working scatter does not prove image linkage: tabular data and image chunks travel through separate paths.