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].

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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.

To install ClearMap see Installation.