ClearMap.pipeline_orchestrators#
Set of classes that each focus on a specific task in the ClearMap pipeline.
The pipeline_orchestrators are the main building blocks of the ClearMap pipeline.
The base class from which all pipeline_orchestrators inherit is TabProcessor.
Then there are 2 types of derived classes, preprocessor and the ones using a preprocessor.
- Note batch_process is not a processor but a set of convenience functions to run aspects of
the pipeline on a group of samples.
Sub-packages and modules#
The processor set of scripts to batch process a group of samples.
Per-channel cell detection, filtering, atlas alignment, and density mapping.
This module provides functionality to run inference on the nature of degree=1 vertices in a vascular graph, detecting tip cells and interrupted vessels.
Coordinator for application flow between configuration, workspace/sample state, and processing workers.
Base classes for all ClearMap processing workers.
Sample-level metadata management, configuration synchronisation, workspace reconciliation, and channel queries.
Vasculature binarization, graph construction, and vessel-type annotation.