ClearMap

ClearMap.Alignment

This sub-package provides an interface to alignment tools in order to register cleared samples to atlases or reference samples.

ClearMap.Analysis

ClearMap analysis and statistics toolbox.

ClearMap.Compile

Script to compile all ClearMap code.

ClearMap.Environment

Initialize a ClearMap environment with all main functionality.

ClearMap.External

Interface to external packages modifed to work with ClearMap.

ClearMap.IO

This module handels data reading and writing in ClearMap via sources and sinks.

ClearMap.ImageProcessing

This sub-package provides routines for volumetric image processing in parallel

ClearMap.ParallelProcessing

This sub-package provides functions for parallel processing of data for ClearMap.

ClearMap.Scripts

Folder containing the main processing pipeline scripts.

ClearMap.Settings

Module to set ClearMap’s internal parameter and paths to external programs.

ClearMap.Tests

A collection of utils nd data for testing.

ClearMap.Utils

Utility functions used throughout ClearMap.

ClearMap.Visualization

This sub-package provides tools for the visualization of the data and analysis results using the vispy library.

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

ClearMap has been designed to analyze O(TB) 3d datasets obtained via light sheet microscopy from iDISCO+ cleared tissue samples immunolabeled for proteins.

ClearMap includes

  • non-ridgid wobbly stitching,

  • image registration to a 3D annotated references (e.g. the Allen Brain Institute Atlases),

  • a toolbox for large volumetric image processing O(TB),

  • object and cell detection,

  • vasculature detection and graph construction,

  • statistical analysis

ClearMap has been written for mapping immediate early genes [Renier2016] as well as vasculature networks of whole mouse brains [Kirst2020].

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.

ClearMap is written in Python 3 and is designed to take advantage of parallel processing capabilities of modern workstations. We hope the open structure of the code will enable many new modules to be added to ClearMap to broaden the range of applications to different types of biological objects or structures.

More informatoin and downloads for ClearMap can be found in our repository.

References

Renier2016

Mapping of brain activity by automated volume analysis of immediate early genes.’Renier* N, Adams* EL, Kirst* C, Wu* Z, et al. Cell. 2016 165(7):1789-802

Kirst2020

Mapping the Fine-Scale Organization and Plasticity of the Brain Vasculature. Kirst, C., Skriabine, S., Vieites-Prado, A., Topilko, T., Bertin, P., Gerschenfeld, G., Verny, F., Topilko, P., Michalski, N., Tessier-Lavigne, M. and Renier, N., Cell, 180(4):780-795