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ClearMap 2.0 with WobblyStitcher, TubeMap and CellMap and new fluorescence functionality

Home Page: https://christophkirst.github.io/ClearMap2Documentation

License: GNU General Public License v3.0

Shell 0.03% C++ 0.12% Python 41.28% Jupyter Notebook 57.85% Cython 0.72%

clearmap2_fluor's Introduction

ClearMap 2.1

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

🆕 This is the new 2.1 version of ClearMap which includes a Graphical User Interface. To use it, make sure that the install_gui.sh script is executable and run it by opening a terminal in the ClearMap2 folder and typing ./run_gui.sh.

2.1.0 what's new

ClearMap's tool box includes

TubeMap

Extract vasculature and other tubular networks from TB data.

CellMap

Extract neuronal activity marker and cell shapes.

Background and Applications

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

ClearMap has been written for mapping immediate early genes Renier et al. Cell 2016 as well as vasculature networks of whole mouse brains Kirst et al. Cell 2020

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.

Installation

Please refer to our documentation on how to install ClearMap.

Tutorials

Tutorials for TubeMap and CellMap are avaialbe as jupyer notebooks:

Documentation

ClearMap comes with a full documentation.

For experimental protocols also refer to idisco.info

News and Media

ClearMap has been featured in differnet articles, interviews and a TEDx talk:

References

See who cites us:

and cite us if you use the sofware in any form:

@article{kirst2020mapping,
   title={Mapping the fine-scale organization and plasticity of the brain vasculature},
   author={Kirst, Christoph and Skriabine, Sophie and Vieites-Prado, Alba and Topilko, Thomas and Bertin, Paul and Gerschenfeld, Gaspard and Verny, Florine and Topilko, Piotr and Michalski, Nicolas and Tessier-Lavigne, Marc and others},
   journal={Cell},
   volume={180},
   number={4},
   pages={780--795},
   year={2020},
   publisher={Elsevier},
   url={https://doi.org/10.1016/j.cell.2016.05.007}}

@article{renier2016mapping,
   title={Mapping of brain activity by automated volume analysis of immediate early genes},
   author={Renier, Nicolas and Adams, Eliza L and Kirst, Christoph and Wu, Zhuhao and Azevedo, Ricardo and Kohl, Johannes and Autry, Anita E and Kadiri, Lolahon and Venkataraju, Kannan Umadevi and Zhou, Yu and others},
   journal={Cell},
   volume={165},
   number={7},
   pages={1789--1802},
   year={2016},
   publisher={Elsevier},
   url={https://doi.org/10.1016/j.cell.2020.01.028}}