High Content Screening
Bases: BaseGroupv04[HCSAttrs]
An OME-Zarr high-content screening (HCS) dataset representing a single plate.
Attributes:
| Name | Type | Description |
|---|---|---|
zarr_format |
Literal[2]
|
|
attributes |
HCSAttrs
|
|
members |
Mapping[str, GroupSpec | ArraySpec] | 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.
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 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. |
Plate metadata
For reference, see the plate section of the OME-Zarr specification.
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 |
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 | None
|
Version of the plate specification |