CLI reference¶
Selecting input positions¶
set-scale and compute-pyramid accept position paths, plate roots, and glob
patterns with -i or --input-position-dirpaths. A plate root selects every
position in the plate. One -i accepts multiple paths, up to the next option.
# All positions in a plate
iohub compute-pyramid -i input.zarr --levels 4
# Positions matching a glob
iohub compute-pyramid -i 'input.zarr/A/*/*' --levels 4
# Two specific positions
iohub set-scale -i input.zarr/A/1/0 input.zarr/B/2/0 -z 2
iohub expands quoted globs. Your shell expands unquoted ones.
To use these options in another Typer CLI, see Options with multiple values.
Commands¶
iohub¶
iohub: N-dimensional bioimaging I/O
Usage¶
iohub [OPTIONS] COMMAND [ARGS]...
Arguments¶
No arguments available
Options¶
| Name | Description | Required | Default |
|---|---|---|---|
-v, --version |
Show the iohub version and exit. | No | - |
--install-completion |
Install completion for the current shell. | No | - |
--show-completion |
Show completion for the current shell, to copy it or customize the installation. | No | - |
Commands¶
| Name | Description |
|---|---|
info |
Show dataset metadata. |
convert |
Convert Micro-Manager TIFF to OME-Zarr, or... |
set-scale |
Update axis scale metadata in OME-Zarr... |
compute-pyramid |
Create or recompute an OME-Zarr pyramid in... |
rename-wells |
Rename wells in an OME-Zarr plate. |
Subcommands¶
info¶
Show dataset metadata.
Accepts Micro-Manager OME-TIFF and NDTIFF datasets, OME-Zarr 0.4 and 0.5 directories, and zipped OME-Zarr archives with the .ozx extension.
Usage¶
iohub info [OPTIONS] {files}...
Arguments¶
| Name | Description | Required |
|---|---|---|
files |
One or more datasets to inspect. | Yes |
Options¶
| Name | Description | Required | Default |
|---|---|---|---|
-v, --verbose |
Show Python usage examples and the full OME-Zarr plate tree. | No | False |
convert¶
Convert Micro-Manager TIFF to OME-Zarr, or pack and unpack .ozx archives.
An .ozx output packs an OME-Zarr directory without changing its chunks. An .ozx input unpacks to a directory. Other inputs use the TIFF converter.
--grid-layout, --chunks, and --num-workers apply only to TIFF conversion. --ome-zarr-version does not apply when unpacking.
Usage¶
iohub convert [OPTIONS]
Arguments¶
No arguments available
Options¶
| Name | Description | Required | Default |
|---|---|---|---|
-i, --input |
Micro-Manager TIFF directory, OME-Zarr directory, or .ozx archive. | Yes | - |
-o, --output |
Output OME-Zarr directory or .ozx archive. | Yes | - |
-g, --grid-layout |
Arrange fields of view in a row/column grid. TIFF conversion only. | No | False |
-c, --chunks |
Chunk shape as 'XY', 'XYZ', or a tuple. 'XYZ' caps chunks at 500 MB. TIFF conversion only. | No | XYZ |
--ome-zarr-version, -v [0.4|0.5] |
OME-NGFF version. Defaults to 0.4 for TIFF conversion or the source version when packing .ozx. | No | - |
-n, --num-workers |
Threads copying pixels concurrently. Defaults to 4; NDTiff scales to about 16. TIFF conversion only. | No | - |
set-scale¶
Update axis scale metadata in OME-Zarr positions.
Omitted axes keep their current scales. Image data is unchanged.
Example:
iohub set-scale -i input.zarr/A/1/0 -z 2.0
Usage¶
iohub set-scale [OPTIONS]
Arguments¶
No arguments available
Options¶
| Name | Description | Required | Default |
|---|---|---|---|
-i, --input-position-dirpaths |
Position paths, plate roots, or globs. A plate root selects all positions. One -i accepts multiple paths, up to the next option. | Yes | - |
-t, --t-scale |
New time-axis scale. | No | - |
-z, --z-scale |
New z-axis scale. | No | - |
-y, --y-scale |
New y-axis scale. | No | - |
-x, --x-scale |
New x-axis scale. | No | - |
--image |
Image to update. Defaults to '0'. | No | - |
compute-pyramid¶
Create or recompute an OME-Zarr pyramid in place.
Level 0 is unchanged. Existing pyramids must have the requested number of levels. Recomputing overwrites the downsampled levels. Every label image under labels/ gets the image's levels, along the axes the image pyramid downsamples (--dims for a new one, the existing one's otherwise), with --label-method: a reducer that never invents values, so the label ids of level 0 are the only ones at the coarser levels.
Example:
iohub compute-pyramid -i input.zarr -l 3 -m median --dims y,x
Usage¶
iohub compute-pyramid [OPTIONS]
Arguments¶
No arguments available
Options¶
| Name | Description | Required | Default |
|---|---|---|---|
-i, --input-position-dirpaths |
Position paths, plate roots, or globs. A plate root selects all positions. One -i accepts multiple paths, up to the next option. | Yes | - |
-l, --levels |
Total number of levels, including the original level 0. | Yes | - |
--method, -m [mean|median|mode|min|max|stride] |
Downsampling method. | No | mean |
-d, --dims |
Comma-separated axes for a new pyramid, such as 'y,x'. Defaults to 'z,y,x'. | No | - |
--label-method [mode|min|max|stride] |
Downsampling method for the position's label images, labels/NAME. | No | max |
--resume |
Skip the pyramid regions an earlier run of this command (same levels, methods and dims) already finished; for retrying an interrupted run. | No | False |
-n, --num-workers |
Threads that downsample each region, one timepoint and channel volume per thread. | No | 1 |
rename-wells¶
Rename wells in an OME-Zarr plate.
Use a CSV with two columns, old name then new name, and no header:
A/1,B/1
A/2,B/2
Example:
iohub rename-wells -i plate.zarr -c names.csv
Usage¶
iohub rename-wells [OPTIONS]
Arguments¶
No arguments available
Options¶
| Name | Description | Required | Default |
|---|---|---|---|
-i, --input |
OME-Zarr plate directory. | Yes | - |
-c, --csv |
CSV file mapping old well names to new names. | Yes | - |