Welcome

ClearMap is a toolbox for the analysis and registration of volumetric data from cleared tissues.

It was initially developed to map brain activity at cellular resolution in whole mouse brains using immediate early gene expression. It has since then been extended as a tool for the qunatification of whole mouse brain vascualtur networks at capilary resolution.

Start reading about ClearMap in this overview or learn about ClearMap's functionality.

Toolbox

TubeMap

Extract vasculature and other tubular networks from TB data with TubeMap

TubeMap

Wobbly Stitcher

Stitch TB data sets non-rigidly with WobblyStitcher

WobblyStitcher

CellMap

Extract neuronal activity marker and cell shapes with CellMap

CellMap

Overview

ClearMap has been designed to analyze O(TB) 3d datasets obtained via light sheet microscopy from iDISCO+ cleared tissue samples immunolabeled for proteins. The ClearMap tools may also be useful for data obtained with other types of microscopes, types of markers, clearing techniques, as well as other species, organs, or samples.

Click here for publications and more details.

Overview

Overview over ClearMap and application.

Documentation

Full api documentation.

Installation

Installation instructions.

Search

Search the ClearMap documentation.

Index

Search the ClearMap documentation.