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`

iohub convert¶

Converts Micro-Manager TIFF datasets to OME-Zarr

Usage:

iohub convert [OPTIONS]

Options:

Name	Type	Description	Default
`-h`, `--help`	boolean	Show this message and exit.	`False`
`--input`, `-i`	directory	Input Micro-Manager TIFF dataset directory	`Sentinel.UNSET`
`--output`, `-o`	path	Output zarr store (/**/converted.zarr)	`Sentinel.UNSET`
`--grid-layout`, `-g`	boolean	Arrange FOVs in a row/column grid layout for tiled acquisition	`False`
`--chunks`, `-c`	text	Zarr chunk size given as 'XY', 'XYZ', or a tuple of chunk dimensions. If 'XYZ', chunk size will be limited to 500 MB.	`XYZ`
`--ome-zarr-version`, `-v`	choice (`0.4` \| `0.5`)	OME-NGFF version for the output Zarr store. '0.4' uses Zarr v2 format, '0.5' uses Zarr v3 format.	`0.4`

iohub info¶

View basic metadata of a list of FILES.

Supported formats are Micro-Manager-acquired TIFF datasets (single-page TIFF, multi-page OME-TIFF, NDTIFF) and OME-Zarr (v0.1 linear HCS layout and all v0.4 layouts).

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`

iohub 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`

iohub 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`