Congratulations Dr. Max!

We are most delighted that Maxime Zimmermann has just passed his PhD viva!

For his thesis, maxime looked at the retinal basis of colour vision in zebrafish, with a key focus on bipolar cells. He also spent much energy building a wide range of open source lab tools, including visual stimulators.

Thank you to Isaac Bianco and Andy Penn for serving as examiners, and Guy Richardson for chairing.

 

Max’s papers so far:

Zimmermann MJY*, Nevala NE*, Yoshimatsu T*, Osorio D, Nilsson DE, Berens P, Baden T§. Zebrafish differentially process colour across visual space to match natural scenes. Current Biology 28(1-15). direct link. (bioRxiv version). pdf.

Zimmermann MJY§, Chagas AM, Bartel P, Pop S, Prieto Godino LL, Baden T§. LED Zappelin’: An open source LED controller for arbitrary spectrum visual stimulation and optogenetics during 2-photon imaging. HardwareX e00127 (bioRxiv version). d

 

 

Congratulations Dr. Phil!

We are most delighted that Philipp Bartel has just passed his PhD viva!

For his thesis, Philipp looked at spectral processing in zebrafish, from cones to brain circuits. Some of his work is already published, with much more to come!

Thank you to Andrew Stockman and Tom Collett for serving as examiners, and Daniel Osorio for chairing.

 

Phil’s papers so far:

Bartel P$, Janiak FK, Osorio D, Baden T$. Colourfulness as a possible measure of object proximity in the larval zebrafish brain. bioRxiv doi: https://doi.org/10.1101/2020.12.03.410241. direct link. pdf.

Yoshimatsu T, Bartel P, Schroeder C, Janiak FK, St-Pierre F, Berens P, Baden T$. Near-optimal rotation of colour space by zebrafish cones in vivo. bioRxiv doi: https://doi.org/10.1101/2020.10.26.356089. direct link. pdf.

Janiak FK§, Bartel P, Bale M, Yoshimatsu T, Komulainen EH, Zhou M, Staras K, Prieto Godino LL, Euler T, Maravall M, Baden T§. Divergent excitation two photon microscopy for 3D random access mesoscale imaging at single cell resolution. bioRxiv doi: https:/doi.org/10.1101/821405. direct link. pdf.

Zimmermann MJY§, Chagas AM, Bartel P, Pop S, Prieto Godino LL, Baden T§. LED Zappelin’: An open source LED controller for arbitrary spectrum visual stimulation and optogenetics during 2-photon imaging. HardwareX e00127 (bioRxiv version). d

Baden T§, James B, Zimmermann M, Bartel P, Griseels D, Lagnado L* and Maravall M*. Spikeling: a low-cost hardware implementation of a spiking neuron for neuroscience teaching and outreach. PLoS Biology  doi.org/10.1371/journal.pbio.2006760. bioRxiv version). direct link. pdf.

Open Hardware efforts featured @Nature Magazine

We are delighted that several of our efforts to promote the use of Open Hardware in Research in Education were featured in a recent Nature Techology Feature by Sandeep Ravindran.

The article takes a sweeping cross-section across several people’s work, highlighting amongst others our work from the lab itself as well as the wider Sussex neuroscience community and our long-standing efforts to promote OH in Africa via TReND.

 

Access the full article here

New lab talk on Worldwide Neuro

On Tuesday 10th Nov 2021 Tom gave an online world-wide neuro seminar, hosted by IST Austra. The talk was recorded can be watched here: https://www.worldwideneuro.com/seminar-event.html?id=1267 

Go directly to video

Abstract
In this talk I will summarize some of our recent unpublished work on spectral coding in the larval zebrafish retina. Combining 2p imaging, hyperspectral stimulation, computational modeling and connectomics, we take a renewed look at the spectral tuning of cone photoreceptors in the live eye. We find that already cones optimally rotate natural colour space in a PCA-like fashion to disambiguate greyscale from “colour” information. We then follow this signal through the retinal layers and ultimately into the brain to explore the major spectral computations performed by the visual system at its consecutive stages. We find that by and large, zebrafish colour vision can be broken into three major spectral zones: long wavelength grey-scale-like vision, short-wavelength prey capture circuits, and spectrally diverse mid-wavelength circuits which possibly support the bulk of “true colour vision” in this tetrachromate vertebrate.

New zebrafish colour vision paper on bioRxiv

Yoshimatsu T, Bartel P, Schroeder C, Janiak FK, St-Pierre F, Berens P, Baden T. Near-optimal rotation of colour space by zebrafish cones in vivo. bioRxiv doi: https://doi.org/10.1101/2020.10.26.356089. direct link. pdf.

For colour vision, retinal circuits must separate information about intensity and wavelength. This requires circuit level comparison of at least two spectrally distinct photoreceptors. However, many vertebrates use four or more, and in those cases the nature and implementation of this computation remains poorly understood. Here, we establish the complete circuit architecture and function of outer retinal circuits underlying colour processing in the tetrachromatic larval zebrafish. Our findings reveal that the specific spectral tunings of the four cone types near optimally rotate the encoding of natural daylight in a principal component analysis (PCA)−like manner to yield one primary achromatic axis, two colour opponent axes as well as a secondary UV-achromatic axis for prey capture. We note that fruit flies − the only other tetrachromat species where comparable circuit-level information is available − use essentially the same strategy to extract spectral information from their relatively blue-shifted terrestrial visual world. Together, our results suggest that rotating colour space into achromatic and chromatic axes at the eye′s first synapse may be a fundamental principle of colour vision when using more than two spectrally well separated photoreceptor types.