Usage

ClearMap is best run through the main Scripts:

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

ClearMap Environment

To make your functions available in your python console run

>>> from ClearMap.Environment import *

Note

When running this for the first time sub-modules will be compiled on demand which can take up to 10-30min.

Example

Here is a simple example that loads a data source and plots it:

>>> from ClearMap.Environment import *
>>> source = io.as_source('path_to_filename')
>>> p3d.plot(source)