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An unbiased template of the Drosophila brain and ventral nerve cord

View ORCID ProfileJohn A Bogovic, View ORCID ProfileHideo Otsuna, Larissa Heinrich, Masayoshi Ito, Jennifer Jeter, View ORCID ProfileGeoffrey Meissner, Aljoscha Nern, Jennifer Colonell, Oz Malkesman, Kei Ito, View ORCID ProfileStephan Saalfeld
doi: https://doi.org/10.1101/376384
John A Bogovic
1Janelia Research Campus, HHMI, Ashburn, VA, USA
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Hideo Otsuna
1Janelia Research Campus, HHMI, Ashburn, VA, USA
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Larissa Heinrich
1Janelia Research Campus, HHMI, Ashburn, VA, USA
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Masayoshi Ito
1Janelia Research Campus, HHMI, Ashburn, VA, USA
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Jennifer Jeter
1Janelia Research Campus, HHMI, Ashburn, VA, USA
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Geoffrey Meissner
1Janelia Research Campus, HHMI, Ashburn, VA, USA
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Aljoscha Nern
1Janelia Research Campus, HHMI, Ashburn, VA, USA
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Jennifer Colonell
1Janelia Research Campus, HHMI, Ashburn, VA, USA
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Oz Malkesman
1Janelia Research Campus, HHMI, Ashburn, VA, USA
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Kei Ito
2Institute of Zoology, University of Cologne, Germany
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Stephan Saalfeld
1Janelia Research Campus, HHMI, Ashburn, VA, USA
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  • For correspondence: saalfelds@janelia.hhmi.org
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Abstract

The fruit fly Drosophila melanogaster is an important model organism for neuroscience with a wide array of genetic tools that enable the mapping of individuals neurons and neural subtypes. Brain templates are essential for comparative biological studies because they enable analyzing many individuals in a common reference space. Several central brain templates exist for Drosophila, but every one is either biased, uses sub-optimal tissue preparation, is imaged at low resolution, or does not account for artifacts. No publicly available Drosophila ventral nerve cord template currently exists. In this work, we created high-resolution templates of the Drosophila brain and ventral nerve cord using the best-available technologies for imaging, artifact correction, stitching, and template construction using groupwise registration. We evaluated our central brain template against the four most competitive, publicly available brain templates and demonstrate that ours enables more accurate registration with fewer local deformations in shorter time.

Footnotes

  • ↵* bogovicj{at}janelia.hhmi.org, saalfelds{at}janelia.hhmi.org

  • We extended evaluation with the registration tool elastix and show that this offers a 10x speedup over CMTK at comparable quality. We developed and describe a new format for transformations that offers >10x compression at minimal loss of precision over existing formats. We developed and describe new open source software to convert between transformation formats including our own and to apply and compare the registrations to image data and geometric data. We added and discussed another metric for local deformation. We added more qualitative examples in the supplement.

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-ND 4.0 International license.
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Posted December 21, 2019.
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An unbiased template of the Drosophila brain and ventral nerve cord
John A Bogovic, Hideo Otsuna, Larissa Heinrich, Masayoshi Ito, Jennifer Jeter, Geoffrey Meissner, Aljoscha Nern, Jennifer Colonell, Oz Malkesman, Kei Ito, Stephan Saalfeld
bioRxiv 376384; doi: https://doi.org/10.1101/376384
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An unbiased template of the Drosophila brain and ventral nerve cord
John A Bogovic, Hideo Otsuna, Larissa Heinrich, Masayoshi Ito, Jennifer Jeter, Geoffrey Meissner, Aljoscha Nern, Jennifer Colonell, Oz Malkesman, Kei Ito, Stephan Saalfeld
bioRxiv 376384; doi: https://doi.org/10.1101/376384

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