segmentation workflows

segmentation workflows#

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

Initialize a processing step and normalize configuration handling.

Parameters:

  • config – Parsed configuration dictionary or path to a config file. If the top-level config contains a key matching the concrete step class name, that sub-dictionary is used as the step config.

  • directory – Working directory for this step.

  • project_location – Project root when running as part of Project.

  • debug – Enable verbose stdout logging in addition to file logging.

  • overwrite – If True, existing step output may be removed before processing.

  • project – Active Project instance when this step is project-managed.

  • filehandler – Shared SpatialData file handler for project-managed runs.

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

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

Initialize a processing step and normalize configuration handling.

Parameters:

  • config – Parsed configuration dictionary or path to a config file. If the top-level config contains a key matching the concrete step class name, that sub-dictionary is used as the step config.

  • directory – Working directory for this step.

  • project_location – Project root when running as part of Project.

  • debug – Enable verbose stdout logging in addition to file logging.

  • overwrite – If True, existing step output may be removed before processing.

  • project – Active Project instance when this step is project-managed.

  • filehandler – Shared SpatialData file handler for project-managed runs.

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

method#

alias of WGASegmentation

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

Initialize a processing step and normalize configuration handling.

Parameters:

  • config – Parsed configuration dictionary or path to a config file. If the top-level config contains a key matching the concrete step class name, that sub-dictionary is used as the step config.

  • directory – Working directory for this step.

  • project_location – Project root when running as part of Project.

  • debug – Enable verbose stdout logging in addition to file logging.

  • overwrite – If True, existing step output may be removed before processing.

  • project – Active Project instance when this step is project-managed.

  • filehandler – Shared SpatialData file handler for project-managed runs.

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

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

Initialize a processing step and normalize configuration handling.

Parameters:

  • config – Parsed configuration dictionary or path to a config file. If the top-level config contains a key matching the concrete step class name, that sub-dictionary is used as the step config.

  • directory – Working directory for this step.

  • project_location – Project root when running as part of Project.

  • debug – Enable verbose stdout logging in addition to file logging.

  • overwrite – If True, existing step output may be removed before processing.

  • project – Active Project instance when this step is project-managed.

  • filehandler – Shared SpatialData file handler for project-managed runs.

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

method#

alias of DAPISegmentation

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

Initialize a processing step and normalize configuration handling.

Parameters:

  • config – Parsed configuration dictionary or path to a config file. If the top-level config contains a key matching the concrete step class name, that sub-dictionary is used as the step config.

  • directory – Working directory for this step.

  • project_location – Project root when running as part of Project.

  • debug – Enable verbose stdout logging in addition to file logging.

  • overwrite – If True, existing step output may be removed before processing.

  • project – Active Project instance when this step is project-managed.

  • filehandler – Shared SpatialData file handler for project-managed runs.

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

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

Initialize a processing step and normalize configuration handling.

Parameters:

  • config – Parsed configuration dictionary or path to a config file. If the top-level config contains a key matching the concrete step class name, that sub-dictionary is used as the step config.

  • directory – Working directory for this step.

  • project_location – Project root when running as part of Project.

  • debug – Enable verbose stdout logging in addition to file logging.

  • overwrite – If True, existing step output may be removed before processing.

  • project – Active Project instance when this step is project-managed.

  • filehandler – Shared SpatialData file handler for project-managed runs.

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

method#

alias of DAPISegmentationCellpose

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

Initialize a processing step and normalize configuration handling.

Parameters:

  • config – Parsed configuration dictionary or path to a config file. If the top-level config contains a key matching the concrete step class name, that sub-dictionary is used as the step config.

  • directory – Working directory for this step.

  • project_location – Project root when running as part of Project.

  • debug – Enable verbose stdout logging in addition to file logging.

  • overwrite – If True, existing step output may be removed before processing.

  • project – Active Project instance when this step is project-managed.

  • filehandler – Shared SpatialData file handler for project-managed runs.

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

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

Initialize a processing step and normalize configuration handling.

Parameters:

  • config – Parsed configuration dictionary or path to a config file. If the top-level config contains a key matching the concrete step class name, that sub-dictionary is used as the step config.

  • directory – Working directory for this step.

  • project_location – Project root when running as part of Project.

  • debug – Enable verbose stdout logging in addition to file logging.

  • overwrite – If True, existing step output may be removed before processing.

  • project – Active Project instance when this step is project-managed.

  • filehandler – Shared SpatialData file handler for project-managed runs.

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

method#

alias of CytosolSegmentationCellpose

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

Initialize a processing step and normalize configuration handling.

Parameters:

  • config – Parsed configuration dictionary or path to a config file. If the top-level config contains a key matching the concrete step class name, that sub-dictionary is used as the step config.

  • directory – Working directory for this step.

  • project_location – Project root when running as part of Project.

  • debug – Enable verbose stdout logging in addition to file logging.

  • overwrite – If True, existing step output may be removed before processing.

  • project – Active Project instance when this step is project-managed.

  • filehandler – Shared SpatialData file handler for project-managed runs.

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

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

Initialize a processing step and normalize configuration handling.

Parameters:

  • config – Parsed configuration dictionary or path to a config file. If the top-level config contains a key matching the concrete step class name, that sub-dictionary is used as the step config.

  • directory – Working directory for this step.

  • project_location – Project root when running as part of Project.

  • debug – Enable verbose stdout logging in addition to file logging.

  • overwrite – If True, existing step output may be removed before processing.

  • project – Active Project instance when this step is project-managed.

  • filehandler – Shared SpatialData file handler for project-managed runs.

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

method#

alias of CytosolOnlySegmentationCellpose

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

Initialize a processing step and normalize configuration handling.

Parameters:

  • config – Parsed configuration dictionary or path to a config file. If the top-level config contains a key matching the concrete step class name, that sub-dictionary is used as the step config.

  • directory – Working directory for this step.

  • project_location – Project root when running as part of Project.

  • debug – Enable verbose stdout logging in addition to file logging.

  • overwrite – If True, existing step output may be removed before processing.

  • project – Active Project instance when this step is project-managed.

  • filehandler – Shared SpatialData file handler for project-managed runs.

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

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

Initialize a processing step and normalize configuration handling.

Parameters:

  • config – Parsed configuration dictionary or path to a config file. If the top-level config contains a key matching the concrete step class name, that sub-dictionary is used as the step config.

  • directory – Working directory for this step.

  • project_location – Project root when running as part of Project.

  • debug – Enable verbose stdout logging in addition to file logging.

  • overwrite – If True, existing step output may be removed before processing.

  • project – Active Project instance when this step is project-managed.

  • filehandler – Shared SpatialData file handler for project-managed runs.

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

method#

alias of CytosolSegmentationDownsamplingCellpose

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

Initialize a processing step and normalize configuration handling.

Parameters:

  • config – Parsed configuration dictionary or path to a config file. If the top-level config contains a key matching the concrete step class name, that sub-dictionary is used as the step config.

  • directory – Working directory for this step.

  • project_location – Project root when running as part of Project.

  • debug – Enable verbose stdout logging in addition to file logging.

  • overwrite – If True, existing step output may be removed before processing.

  • project – Active Project instance when this step is project-managed.

  • filehandler – Shared SpatialData file handler for project-managed runs.

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

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

Initialize a processing step and normalize configuration handling.

Parameters:

  • config – Parsed configuration dictionary or path to a config file. If the top-level config contains a key matching the concrete step class name, that sub-dictionary is used as the step config.

  • directory – Working directory for this step.

  • project_location – Project root when running as part of Project.

  • debug – Enable verbose stdout logging in addition to file logging.

  • overwrite – If True, existing step output may be removed before processing.

  • project – Active Project instance when this step is project-managed.

  • filehandler – Shared SpatialData file handler for project-managed runs.

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

method#

alias of CytosolOnlySegmentationDownsamplingCellpose

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