Aligning spikes to histology with BrainGlobe

Alessandro Felder & Adam Tyson

Sainsbury Wellcome Centre & Gatsby Computational Neuroscience Unit, UCL.

Aligning spikes to histology

  • Record from 100’s of cells at once
  • Need to know where these recordings are from
  • Need to combine recordings from multiple animals

Probe track labelling & imaging

 

Tyson, A. L. et al. (2022) “Accurate determination of marker location within whole-brain microscopy images” Sci Rep, 12, 867

Atlas alignment

Tyson, A. L. et al. (2022) “Accurate determination of marker location within whole-brain microscopy images” Sci Rep, 12, 867

brainreg & brainglobe-segmentation

Tyson, A. L. et al. (2022) “Accurate determination of marker location within whole-brain microscopy images” Sci Rep, 12, 867

Validation

Tyson, A. L., Vélez-Fort, M., Rousseau, C. V. et al. (2022) “Accurate determination of marker location within whole-brain microscopy images” Scientific Reports, 12, 867

Demo

Output

Position Region ID Region acronym Region name
0 593 VISp1 Primary visual area, layer 1
1 593 VISp1 Primary visual area, layer 1
2 593 VISp1 Primary visual area, layer 1
…
55 821 VISp2/3 Primary visual area, layer 2/3
56 821 VISp2/3 Primary visual area, layer 2/3
…
998 632 DG-sg Dentate gyrus, granule cell layer
999 632 DG-sg Dentate gyrus, granule cell layer

Other structures

Tyson, A. L., Vélez-Fort, M., Rousseau, C. V. et al. (2022) “Accurate determination of marker location within whole-brain microscopy images” Scientific Reports, 12, 867

BrainGlobe

BrainGlobe Atlas API

Claudi, F. et al. (2020) “BrainGlobe Atlas API: a common interface for neuroanatomical atlases” JOSS, v5(54), 2668

Current atlases

Atlas Name Resolution Ages Reference Images
Allen Mouse Brain Atlas 10, 25, 50, and 100 micron P56 STPT
Allen Human Brain Atlas 500 micron Adult MRI
Max Planck Zebrafish Brain Atlas 1 micron 6-dpf FISH
Enhanced and Unified Mouse Brain Atlas 10, 25, 50, and 100 micron P56 STPT
Smoothed version of the Kim et al. mouse reference atlas 10, 25, 50 and 100 micron P56 STPT
Gubra’s LSFM mouse brain atlas 20 micron 8 to 10 weeks post natal LSFM
3D version of the Allen mouse spinal cord atlas 20 x 10 x 10 micron Adult Nissl
AZBA: A 3D Adult Zebrafish Brain Atlas 4 micron 15-16 weeks post natal LSFM
Waxholm Space atlas of the Sprague Dawley rat brain 39 micron P80 MRI
3D Edge-Aware Refined Atlases Derived from the Allen Developing Mouse Brain Atlases 16, 16.75, and 25 micron E13, E15, E18, P4, P14, P28 & P56 Nissl
Princeton Mouse Brain Atlas 20 micron >P56 (older animals included) LSFM
Kim Lab Developmental CCF 10 micron P56 STP, LSFM (iDISCO) and MRI (a0, adc, dwo, fa, MTR, T2)
Blind Mexican Cavefish Brain Atlas 2 micron 6-dpf IHC
BlueBrain Barrel Cortex Atlas 10 and 25 micron P56 STPT
UNAM Axolotl Brain Atlas 40 micron ~ 3 months post hatching MRI

Claudi, F. et al. (2020) “BrainGlobe Atlas API: a common interface for neuroanatomical atlases” JOSS, v5(54), 2668

Support

Contributors

Stephen Lenzi, Rob Campbell, Joe Ziminski, Sofia Miñano, Niko Sirmpilatze, Nicholas Del Grosso, Laura Porta, Lee Cossell, Antonin Blot, David Pérez-Suárez, David Stansby, Will Graham, Patrick Roddy, Adrien Berchet, Mathieu Bourdenx, Ben Kantor, NovaFae, David Young, Sam Clothier, Gubra-ApS, Kailyn Fields, ramroomh, Samuel Diebolt, Chris Roat, Oren Amsalem, kclamar, Draga Doncila Pop, juanma9613, Jules Scholler, Iaroslavna Vasylieva, Nicolas Peschke, Justin Kiggins, Peter Sobolewski, Simão Bolota, chili-chiu, jaimergp, Sebastian Lammers, Matt Colligan, Paul Brodersen, Carter Peene, francesshei, Sean Martin, Adam Tyson, Federico Claudi, Luigi Petrucco, Christian Niedworok, Charly Rousseau, Horst Obenhaus, Chryssanthi Tsitoura, Sepiedeh Keshavarzi, Mateo Vélez-Fort, Ben Dichter, 4iar, Marco Musy, Anna Medyukhina, stegiopast, EmanPaoli, lidakanari, Alexis Arnaudon, Yaroslav Halchenko, Ziyang Liu, Philip Shamash, koushik-ms, Harald Reingruber, Emily Jane Dennis, Peak, Maximilian Blacher, Hernando Martinez Vergara, Estelle, nicole-vissers, GD, Michael Kunst, Estelle Nassar, Sara Mederos, Igor Tatarnikov, Viktor Plattner, Carlo Castoldi, Jingjie Li, Guillaume Le Goc, Harry Carey, Matt Einhorn, Kimberly Meechan, Robert Kozol, Roberto, Axel Bisi, Jung Woo Kim, Saima Abdus, Saarah Hussain

Resources

BrainGlobe website: brainglobe.info

GitHub: github.com/brainglobe

Tutorial: brainglobe.info/tutorials/silicon-probe-tracking

Contact

Help forum: forum.image.sc

Developer forum: brainglobe.zulipchat.com

brainglobe.info