CLI Reference¶

iohub¶

iohub: N-dimensional bioimaging I/O

Usage:

iohub [OPTIONS] COMMAND [ARGS]...

Options:

Name	Type	Description	Default
`-h`, `--help`	boolean	Show this message and exit.	`False`
`--version`	boolean	Show the version and exit.	`False`

compute-pyramid¶

Compute multiscale pyramid levels in place for OME-Zarr positions.

The level 0 array is preserved; new downsampled levels are appended.

iohub compute-pyramid -i input.zarr/*/*/* --levels 4
iohub compute-pyramid -i input.zarr/*/*/* -l 3 -m median --dims y,x

Usage:

iohub compute-pyramid [OPTIONS]

Options:

Name	Type	Description	Default
`-h`, `--help`	boolean	Show this message and exit.	`False`
`--input-position-dirpaths`, `-i`	tuple	List of paths to input positions, each with the same TCZYX shape. Supports wildcards e.g. 'input.zarr///*'.	`Sentinel.UNSET`
`--levels`, `-l`	integer range (`2` and above)	Total number of pyramid levels including level 0 (e.g. 4 = level 0 + 3 extra).	`Sentinel.UNSET`
`--method`, `-m`	choice (`mean` \| `median` \| `mode` \| `min` \| `max` \| `stride`)	The Downsampling method.	`mean`
`--dims`, `-d`	text	Comma-separated axes to downsample (e.g. 'y,x' for YX-only). Defaults to 'z,y,x'.	None

convert¶

Convert datasets between supported formats.

Routes by suffix: a TIFF directory plus a .zarr output runs the Micro-Manager TIFF → OME-Zarr converter; a .zarr source plus a .ozx output packs an RFC-9 zip archive; a .ozx source plus a .zarr output unpacks back to a directory store.

Usage:

iohub convert [OPTIONS]

Options:

Name	Type	Description	Default
`-h`, `--help`	boolean	Show this message and exit.	`False`
`--input`, `-i`	path	Input dataset: Micro-Manager TIFF dir, OME-Zarr dir, or RFC-9 .ozx archive.	`Sentinel.UNSET`
`--output`, `-o`	path	Output path. Suffix selects the operation: .zarr (Zarr dir) or .ozx (zipped).	`Sentinel.UNSET`
`--grid-layout`, `-g`	boolean	(TIFF → Zarr only) Arrange FOVs in a row/column grid layout.	`False`
`--chunks`, `-c`	text	(TIFF → Zarr only) Zarr chunk size: 'XY', 'XYZ', or a tuple. 'XYZ' caps at 500 MB.	`XYZ`
`--ome-zarr-version`, `-v`	choice (`0.4` \| `0.5`)	OME-NGFF version. TIFF default: 0.4. Pack: sniffed from source if omitted.	None

info¶

View metadata for one or more FILES.

Supports Micro-Manager TIFF datasets (multi-page OME-TIFF, NDTIFF), OME-Zarr directory stores (v0.4 and v0.5), and RFC-9 zipped OME-Zarr archives (.ozx).

Usage:

iohub info [OPTIONS] FILES...

Options:

Name	Type	Description	Default
`-h`, `--help`	boolean	Show this message and exit.	`False`
`--verbose`, `-v`	boolean	Show usage guide to open dataset in Python and full tree for HCS Plates in OME-Zarr	`False`

rename-wells¶

Rename wells in an plate.

iohub rename-wells -i plate.zarr -c names.csv

The CSV file must have two columns with old and new names in the form:

A / 1, B / 2
A / 2, B / 2

Usage:

iohub rename-wells [OPTIONS]

Options:

Name	Type	Description	Default
`-h`, `--help`	boolean	Show this message and exit.	`False`
`-i`, `--input`	path	Path to the input Zarr file.	`Sentinel.UNSET`
`-c`, `--csv`	file	Path to the CSV file containing old and new well names.	`Sentinel.UNSET`

set-scale¶

Update scale metadata in OME-Zarr datasets.

iohub set-scale -i input.zarr/*/*/* -t 1.0 -z 1.0 -y 0.5 -x 0.5

Supports setting a single axis at a time:

iohub set-scale -i input.zarr/*/*/* -z 2.0

Usage:

iohub set-scale [OPTIONS]

Options:

Name	Type	Description	Default
`-h`, `--help`	boolean	Show this message and exit.	`False`
`--input-position-dirpaths`, `-i`	tuple	List of paths to input positions, each with the same TCZYX shape. Supports wildcards e.g. 'input.zarr///*'.	`Sentinel.UNSET`
`--t-scale`, `-t`	float	New t scale	`Sentinel.UNSET`
`--z-scale`, `-z`	float	New z scale	`Sentinel.UNSET`
`--y-scale`, `-y`	float	New y scale	`Sentinel.UNSET`
`--x-scale`, `-x`	float	New x scale	`Sentinel.UNSET`
`--image`	text	Image name to set scale for. Default is '0'	`Sentinel.UNSET`