Overview#

Introduction#

ClearMap is an open-source toolbox for the analysis and registration of volumetric data from cleared tissues.

ClearMap is designed to analyse terabyte-sized 3-D datasets obtained via light sheet microscopy from iDISCO+ cleared tissue samples immunolabeled for proteins. It has been written for mapping immediate early genes [Renier2016] as well as vasculature networks of whole mouse brains [Kirst2020].

Hint

ClearMap tools may also be useful for data obtained with other types of microscopes, markers, clearing techniques, species, organs, or samples.

_images/cell_abstract_2016.jpg _images/cell_abstract_2020.jpg

ClearMap 3.1 extends the original cell-detection and vasculature pipelines with:

  • a GUI for interactive analysis without scripting,

  • a YAML-based configuration system with schema validation,

  • a channel-centred workspace that organises all intermediate and final outputs automatically,

  • myelinated-tract mapping (TractMap) and multi-channel colocalization pipelines,

  • atlas landmark-based registration refinement,

  • group analysis and batch processing for multi-sample studies.

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

Functionality and Pipelines#

ClearMap provides a large set of high-performance 3-D image processing functions described in Package Organisation.

These functions are combined in expert modules under Experts, which are orchestrated by the pipeline workers in pipeline_orchestrators.

The main pipelines are:

Pipeline

Purpose

Documentation

Stitching

Non-rigid stitching of tiled acquisitions

WobblyStitcher

CellMap

Cell detection, atlas alignment, density mapping

CellMap

TubeMap

Vasculature binarization, graph construction, annotation

TubeMap

TractMap

Myelinated-tract binarization and coordinate mapping

(see tract_map)

Colocalization

Multi-channel overlap quantification

(see colocalization)

Group analysis

Batch processing, group comparisons, statistics

(see group_orchestrators)

Usage#

An introduction to how to use ClearMap can be found here: Usage.

Documentation#

The full code documentation can be found here:

ClearMap Documentation

Source#

ClearAnatomics/ClearMap

Authors#

Lead programming and design#

Christoph Kirst and Charly Rousseau

Scripts and specific applications#

Nicolas Renier and Christoph Kirst

Vessel filling network#

Sophie Skriabine, Christoph Kirst, Maxime Boyer

GUI, pipeline orchestrators, and configuration system#

Charly Rousseau

Colocalization module#

Gaël Cousin and Charly Rousseau

Documentation#

Christoph Kirst, Nicolas Renier, Charly Rousseau, Louise Mathé, Gabriele Lienhard, Daniela Domingues

License#

GNU GENERAL PUBLIC LICENSE Version 3

See LICENSE or gnu.org for details.

Social Media#