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Tools for accurate post hoc determination of marker location within whole-brain microscopy images

View ORCID ProfileAdam L. Tyson, Mateo Vélez-Fort, Charly V. Rousseau, Lee Cossell, Chryssanthi Tsitoura, Horst A. Obenhaus, Federico Claudi, Stephen C. Lenzi, Tiago Branco, Troy W. Margrie
doi: https://doi.org/10.1101/2021.05.21.445133
Adam L. Tyson
1Sainsbury Wellcome Centre, University College London, London, United Kingdom
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  • ORCID record for Adam L. Tyson
Mateo Vélez-Fort
1Sainsbury Wellcome Centre, University College London, London, United Kingdom
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Charly V. Rousseau
1Sainsbury Wellcome Centre, University College London, London, United Kingdom
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Lee Cossell
1Sainsbury Wellcome Centre, University College London, London, United Kingdom
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Chryssanthi Tsitoura
1Sainsbury Wellcome Centre, University College London, London, United Kingdom
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Horst A. Obenhaus
2Kavli Institute for Systems Neuroscience and Centre for Neural Computation, Norwegian University of Science and Technology, Trondheim, Norway
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Federico Claudi
1Sainsbury Wellcome Centre, University College London, London, United Kingdom
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Stephen C. Lenzi
1Sainsbury Wellcome Centre, University College London, London, United Kingdom
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Tiago Branco
1Sainsbury Wellcome Centre, University College London, London, United Kingdom
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Troy W. Margrie
1Sainsbury Wellcome Centre, University College London, London, United Kingdom
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  • For correspondence: t.margrie@ucl.ac.uk
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Abstract

To interpret in vivo experiments designed to understand brain function, high-resolution whole-brain microscopy provides a means for post hoc determination of the location of implanted devices and recorded cells in three dimensional brain space that is a critical step for data interrogation. Here we have developed Python-based tools (brainreg and brainreg-segment) to accurately map, in a common coordinate space, the position of dye-labelled probe tracks and two-photon imaged cell populations expressing fluorescent protein. The precise location of probes and cells were validated using physiological recordings and human raters that indicate accuracy levels to less than 70µm. These flexible, open-source methodologies are expected to further evolve with need and to deliver the anatomical precision that is necessary for understanding the functional architecture of the brain.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted May 23, 2021.
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Tools for accurate post hoc determination of marker location within whole-brain microscopy images
Adam L. Tyson, Mateo Vélez-Fort, Charly V. Rousseau, Lee Cossell, Chryssanthi Tsitoura, Horst A. Obenhaus, Federico Claudi, Stephen C. Lenzi, Tiago Branco, Troy W. Margrie
bioRxiv 2021.05.21.445133; doi: https://doi.org/10.1101/2021.05.21.445133
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Tools for accurate post hoc determination of marker location within whole-brain microscopy images
Adam L. Tyson, Mateo Vélez-Fort, Charly V. Rousseau, Lee Cossell, Chryssanthi Tsitoura, Horst A. Obenhaus, Federico Claudi, Stephen C. Lenzi, Tiago Branco, Troy W. Margrie
bioRxiv 2021.05.21.445133; doi: https://doi.org/10.1101/2021.05.21.445133

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