Usage

GUI

The simplest way to use ClearMap is to run the Graphical User Interface (GUI) by typing:

# Replace ClearMapUi39 with your environment name
# This is printed at the end of the installation script for reference
conda activate ClearMapUi39
clearmap-ui

Alternative scripts

Alternatively, you can use the following scripts to run the main functions of ClearMap: cell_map_new_api and tube_map_new_api. [1]

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)

[1]

Deprecated since version 2.1.0: The Former CellMap and TubeMap scripts are now deprecated. For standard uses, see the GUI, or use the new cell_map_new_api and tube_map_new_api scripts.

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