download_images#

Workflow for downloading images from Quilt.

Image metadata is loaded from the Quilt package and used to filter for FOVs with the specified number of cells. FOVs are selected to meet the specified number of FOVs within each cell volume bin. For each selected FOV, the image is downloaded to the working location under images.

Flows

run_flow

Main download images flow.

run_flow(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfig) → None[source]#: Main download images flow.

Configs

`ContextConfig`	Context configuration for download images flow.
`ParametersConfig`	Parameter configuration for download images flow.
`SeriesConfig`	Series configuration for download images flow.

class ContextConfig[source]#

Context configuration for download images flow.

working_location: str#: Location for input and output files (local path or S3 bucket).

metadata_location: str#: Location of metadata file (local path or S3 bucket).

class ParametersConfig[source]#

Parameter configuration for download images flow.

cells_per_fov: int#: Number of cells per FOV.

bins: list[int]#: Cell volume bin boundaries.

counts: list[int]#: Number of FOVs to select from each cell volume bin.

quilt_package: str = 'aics/hipsc_single_cell_image_dataset'#: Name of Quilt package.

quilt_registry: str = 's3://allencell'#: Name of Quilt registry.

class SeriesConfig[source]#

Series configuration for download images flow.

name: str#: Name of the simulation series.

metadata_key: str#: Key for metadata file.