segmentation workflows

class scportrait.pipeline.segmentation.workflows.WGASegmentation(*args, **kwargs)

Initialize a segmentation step.

Parameters:

• config – Step configuration.

• directory – Working directory for this segmentation step.

• nuc_seg_name – Name of the nucleus segmentation output.

• cyto_seg_name – Name of the cytosol segmentation output.

• _tmp_image_path – Path to the temporary input image memmap.

• project_location – Project root path.

• debug – Enable verbose logging.

• overwrite – Whether existing outputs may be overwritten.

• project – Active project instance when project-managed.

• filehandler – Shared SpatialData file handler.

• from_project – Whether this step is invoked from a project-managed context.

• dummy – If True, initialize without cleaning the existing log file. This is used for side-effect-free helper instances that only inspect configuration-derived state.

class scportrait.pipeline.segmentation.workflows.ShardedWGASegmentation(*args, **kwargs)

Initialize a segmentation step.

Parameters:

• config – Step configuration.

• directory – Working directory for this segmentation step.

• nuc_seg_name – Name of the nucleus segmentation output.

• cyto_seg_name – Name of the cytosol segmentation output.

• _tmp_image_path – Path to the temporary input image memmap.

• project_location – Project root path.

• debug – Enable verbose logging.

• overwrite – Whether existing outputs may be overwritten.

• project – Active project instance when project-managed.

• filehandler – Shared SpatialData file handler.

• from_project – Whether this step is invoked from a project-managed context.

• dummy – If True, initialize without cleaning the existing log file. This is used for side-effect-free helper instances that only inspect configuration-derived state.

method

alias of WGASegmentation

class scportrait.pipeline.segmentation.workflows.DAPISegmentation(*args, **kwargs)

Initialize a segmentation step.

Parameters:

• config – Step configuration.

• directory – Working directory for this segmentation step.

• nuc_seg_name – Name of the nucleus segmentation output.

• cyto_seg_name – Name of the cytosol segmentation output.

• _tmp_image_path – Path to the temporary input image memmap.

• project_location – Project root path.

• debug – Enable verbose logging.

• overwrite – Whether existing outputs may be overwritten.

• project – Active project instance when project-managed.

• filehandler – Shared SpatialData file handler.

• from_project – Whether this step is invoked from a project-managed context.

• dummy – If True, initialize without cleaning the existing log file. This is used for side-effect-free helper instances that only inspect configuration-derived state.

class scportrait.pipeline.segmentation.workflows.ShardedDAPISegmentation(*args, **kwargs)

Initialize a segmentation step.

Parameters:

• config – Step configuration.

• directory – Working directory for this segmentation step.

• nuc_seg_name – Name of the nucleus segmentation output.

• cyto_seg_name – Name of the cytosol segmentation output.

• _tmp_image_path – Path to the temporary input image memmap.

• project_location – Project root path.

• debug – Enable verbose logging.

• overwrite – Whether existing outputs may be overwritten.

• project – Active project instance when project-managed.

• filehandler – Shared SpatialData file handler.

• from_project – Whether this step is invoked from a project-managed context.

• dummy – If True, initialize without cleaning the existing log file. This is used for side-effect-free helper instances that only inspect configuration-derived state.

method

alias of DAPISegmentation

class scportrait.pipeline.segmentation.workflows.DAPISegmentationCellpose(*args, **kwargs)

Initialize a segmentation step.

Parameters:

• config – Step configuration.

• directory – Working directory for this segmentation step.

• nuc_seg_name – Name of the nucleus segmentation output.

• cyto_seg_name – Name of the cytosol segmentation output.

• _tmp_image_path – Path to the temporary input image memmap.

• project_location – Project root path.

• debug – Enable verbose logging.

• overwrite – Whether existing outputs may be overwritten.

• project – Active project instance when project-managed.

• filehandler – Shared SpatialData file handler.

• from_project – Whether this step is invoked from a project-managed context.

• dummy – If True, initialize without cleaning the existing log file. This is used for side-effect-free helper instances that only inspect configuration-derived state.

class scportrait.pipeline.segmentation.workflows.ShardedDAPISegmentationCellpose(*args, **kwargs)

Initialize a segmentation step.

Parameters:

• config – Step configuration.

• directory – Working directory for this segmentation step.

• nuc_seg_name – Name of the nucleus segmentation output.

• cyto_seg_name – Name of the cytosol segmentation output.

• _tmp_image_path – Path to the temporary input image memmap.

• project_location – Project root path.

• debug – Enable verbose logging.

• overwrite – Whether existing outputs may be overwritten.

• project – Active project instance when project-managed.

• filehandler – Shared SpatialData file handler.

• from_project – Whether this step is invoked from a project-managed context.

• dummy – If True, initialize without cleaning the existing log file. This is used for side-effect-free helper instances that only inspect configuration-derived state.

method

alias of DAPISegmentationCellpose

class scportrait.pipeline.segmentation.workflows.CytosolSegmentationCellpose(*args, **kwargs)

Initialize a segmentation step.

Parameters:

• config – Step configuration.

• directory – Working directory for this segmentation step.

• nuc_seg_name – Name of the nucleus segmentation output.

• cyto_seg_name – Name of the cytosol segmentation output.

• _tmp_image_path – Path to the temporary input image memmap.

• project_location – Project root path.

• debug – Enable verbose logging.

• overwrite – Whether existing outputs may be overwritten.

• project – Active project instance when project-managed.

• filehandler – Shared SpatialData file handler.

• from_project – Whether this step is invoked from a project-managed context.

• dummy – If True, initialize without cleaning the existing log file. This is used for side-effect-free helper instances that only inspect configuration-derived state.

class scportrait.pipeline.segmentation.workflows.ShardedCytosolSegmentationCellpose(*args, **kwargs)

Initialize a segmentation step.

Parameters:

• config – Step configuration.

• directory – Working directory for this segmentation step.

• nuc_seg_name – Name of the nucleus segmentation output.

• cyto_seg_name – Name of the cytosol segmentation output.

• _tmp_image_path – Path to the temporary input image memmap.

• project_location – Project root path.

• debug – Enable verbose logging.

• overwrite – Whether existing outputs may be overwritten.

• project – Active project instance when project-managed.

• filehandler – Shared SpatialData file handler.

• from_project – Whether this step is invoked from a project-managed context.

• dummy – If True, initialize without cleaning the existing log file. This is used for side-effect-free helper instances that only inspect configuration-derived state.

method

alias of CytosolSegmentationCellpose

class scportrait.pipeline.segmentation.workflows.CytosolOnlySegmentationCellpose(*args, **kwargs)

Initialize a segmentation step.

Parameters:

• config – Step configuration.

• directory – Working directory for this segmentation step.

• nuc_seg_name – Name of the nucleus segmentation output.

• cyto_seg_name – Name of the cytosol segmentation output.

• _tmp_image_path – Path to the temporary input image memmap.

• project_location – Project root path.

• debug – Enable verbose logging.

• overwrite – Whether existing outputs may be overwritten.

• project – Active project instance when project-managed.

• filehandler – Shared SpatialData file handler.

• from_project – Whether this step is invoked from a project-managed context.

• dummy – If True, initialize without cleaning the existing log file. This is used for side-effect-free helper instances that only inspect configuration-derived state.

class scportrait.pipeline.segmentation.workflows.ShardedCytosolOnlySegmentationCellpose(*args, **kwargs)

Initialize a segmentation step.

Parameters:

• config – Step configuration.

• directory – Working directory for this segmentation step.

• nuc_seg_name – Name of the nucleus segmentation output.

• cyto_seg_name – Name of the cytosol segmentation output.

• _tmp_image_path – Path to the temporary input image memmap.

• project_location – Project root path.

• debug – Enable verbose logging.

• overwrite – Whether existing outputs may be overwritten.

• project – Active project instance when project-managed.

• filehandler – Shared SpatialData file handler.

• from_project – Whether this step is invoked from a project-managed context.

• dummy – If True, initialize without cleaning the existing log file. This is used for side-effect-free helper instances that only inspect configuration-derived state.

method

alias of CytosolOnlySegmentationCellpose

class scportrait.pipeline.segmentation.workflows.CytosolSegmentationDownsamplingCellpose(*args, **kwargs)

Initialize a segmentation step.

Parameters:

• config – Step configuration.

• directory – Working directory for this segmentation step.

• nuc_seg_name – Name of the nucleus segmentation output.

• cyto_seg_name – Name of the cytosol segmentation output.

• _tmp_image_path – Path to the temporary input image memmap.

• project_location – Project root path.

• debug – Enable verbose logging.

• overwrite – Whether existing outputs may be overwritten.

• project – Active project instance when project-managed.

• filehandler – Shared SpatialData file handler.

• from_project – Whether this step is invoked from a project-managed context.

• dummy – If True, initialize without cleaning the existing log file. This is used for side-effect-free helper instances that only inspect configuration-derived state.

class scportrait.pipeline.segmentation.workflows.ShardedCytosolSegmentationDownsamplingCellpose(*args, **kwargs)

Initialize a segmentation step.

Parameters:

• config – Step configuration.

• directory – Working directory for this segmentation step.

• nuc_seg_name – Name of the nucleus segmentation output.

• cyto_seg_name – Name of the cytosol segmentation output.

• _tmp_image_path – Path to the temporary input image memmap.

• project_location – Project root path.

• debug – Enable verbose logging.

• overwrite – Whether existing outputs may be overwritten.

• project – Active project instance when project-managed.

• filehandler – Shared SpatialData file handler.

• from_project – Whether this step is invoked from a project-managed context.

• dummy – If True, initialize without cleaning the existing log file. This is used for side-effect-free helper instances that only inspect configuration-derived state.

method

alias of CytosolSegmentationDownsamplingCellpose

class scportrait.pipeline.segmentation.workflows.CytosolOnlySegmentationDownsamplingCellpose(*args, **kwargs)

Initialize a segmentation step.

Parameters:

• config – Step configuration.

• directory – Working directory for this segmentation step.

• nuc_seg_name – Name of the nucleus segmentation output.

• cyto_seg_name – Name of the cytosol segmentation output.

• _tmp_image_path – Path to the temporary input image memmap.

• project_location – Project root path.

• debug – Enable verbose logging.

• overwrite – Whether existing outputs may be overwritten.

• project – Active project instance when project-managed.

• filehandler – Shared SpatialData file handler.

• from_project – Whether this step is invoked from a project-managed context.

• dummy – If True, initialize without cleaning the existing log file. This is used for side-effect-free helper instances that only inspect configuration-derived state.

class scportrait.pipeline.segmentation.workflows.ShardedCytosolOnlySegmentationDownsamplingCellpose(*args, **kwargs)

Initialize a segmentation step.

Parameters:

• config – Step configuration.

• directory – Working directory for this segmentation step.

• nuc_seg_name – Name of the nucleus segmentation output.

• cyto_seg_name – Name of the cytosol segmentation output.

• _tmp_image_path – Path to the temporary input image memmap.

• project_location – Project root path.

• debug – Enable verbose logging.

• overwrite – Whether existing outputs may be overwritten.

• project – Active project instance when project-managed.

• filehandler – Shared SpatialData file handler.

• from_project – Whether this step is invoked from a project-managed context.

• dummy – If True, initialize without cleaning the existing log file. This is used for side-effect-free helper instances that only inspect configuration-derived state.

method

alias of CytosolOnlySegmentationDownsamplingCellpose