High Content Screening

Warning

The implementation of OME-Zarr 0.6 is not final, and subject to change. It is provided so users can test and evaluate ome-zarr-models and the specification before it becomes final. Please report issues and provide feedback!

ome_zarr_models.v06.hcs.HCS

Bases: BaseGroupv06[HCSAttrs]

An OME-Zarr high content screening (HCS) dataset.

Attributes:

Name	Type	Description
`zarr_format`	`Literal[3]`
`node_type`	`Literal['group']`
`attributes`	`BaseZarrAttrs[HCSAttrs]`
`members`	`Mapping[str, GroupSpec \| ArraySpec] \| None`

n_wells

n_wells: int

Number of wells.

well_groups

well_groups: Generator[Well, None, None]

Well groups within this HCS group.

Notes

Only well groups that exist are returned. This can be less than the number of wells defined in the HCS metadata if some of the well Zarr groups don't exist.

from_zarr

from_zarr(group: Group) -> Self

Create an OME-Zarr image model from a zarr.Group.

Parameters:

Name	Type	Description	Default
`group`	`Group`	A Zarr group that has valid OME-Zarr image metadata.	required

get_well_group

get_well_group(i: int) -> Well

Get a single well group.

Parameters:

Name	Type	Description	Default
`i`	`int`	Index of well group.	required

Raises:

Type	Description
`WellGroupNotFoundError`	If no Zarr group is found at the well path.

ome_zarr_models.v06.hcs.HCSAttrs

Bases: BaseOMEAttrs

HCS metadtata attributes.

Attributes:

Name	Type	Description
`version`	`Literal['0.6.dev4']`
`plate`	`Plate`

Plate metadata

For reference, see the plate section of the OME-Zarr specification.

ome_zarr_models.v06.plate.Acquisition

Bases: BaseAttrs

A single acquisition.

Attributes:

Name	Type	Description
`id`	`int`	A unique identifier.
`name`	`str \| None`
`maximumfieldcount`	`int \| None`	Maximum number of fields of view for the acquisition
`description`	`str \| None`
`starttime`	`int \| None`	Integer epoch timestamp of acquisition start time
`endtime`	`int \| None`	Integer epoch timestamp of acquisition end time

ome_zarr_models.v06.plate.Column

Bases: BaseAttrs

A single column within a well.

Attributes:

Name	Type	Description
`name`	`str`

ome_zarr_models.v06.plate.Plate

Bases: PlateBase

A single plate.

Attributes:

Name	Type	Description
`acquisitions`	`list[Acquisition] \| None`
`columns`	`list[Column]`
`field_count`	`int \| None`	Maximum number of fields per view across wells
`name`	`str \| None`	Plate name
`rows`	`list[Row]`
`wells`	`list[WellInPlate]`
`version`	`str`	Version of the plate specification

ome_zarr_models.v06.plate.PlateBase

Bases: BaseAttrs

A single plate.

Attributes:

Name	Type	Description
`acquisitions`	`list[Acquisition] \| None`
`columns`	`list[Column]`
`field_count`	`int \| None`	Maximum number of fields per view across wells
`name`	`str \| None`	Plate name
`rows`	`list[Row]`
`wells`	`list[WellInPlate]`

ome_zarr_models.v06.plate.Row

Bases: BaseAttrs

A single row within a well.

Attributes:

Name	Type	Description
`name`	`str`

ome_zarr_models.v06.plate.WellInPlate

Bases: BaseAttrs

A single well within a plate.

Attributes:

Name	Type	Description
`path`	`str`
`rowIndex`	`int`
`columnIndex`	`int`