ClearMap.Scripts

Folder containing the main processing pipeline scripts.

Scripts include:

Script	Description
CellMap	Cell detection pipeline, e.g. for immediate early gene mapping
TubeMap	Vasculature network construction pipeline

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Sub-packages and modules

ClearMap.Scripts.CellMap	This script is the main pipeline to analyze immediate early gene expression data from iDISCO+ cleared tissue [Renier2016].
ClearMap.Scripts.TubeMap	This script is the main pipeline to generate annotated graphs from vasculature lightsheet data [Kirst2020].
ClearMap.Scripts.align_new_api
ClearMap.Scripts.cell_map_new_api	Headless entry point for the CellMap pipeline (cell detection and density mapping).
ClearMap.Scripts.clearmap_utils
ClearMap.Scripts.create_distance_file
ClearMap.Scripts.generate_jsonl_file_ontology
ClearMap.Scripts.partial_gt_load_demo	A simple demo script to test partial loading of graph properties from a .gt file.
ClearMap.Scripts.tract_map
ClearMap.Scripts.tube_map_new_api	Headless entry point for the TubeMap pipeline (vasculature binarization, graph construction, and annotation).