My group is using machine learning and data analytics for large-scale neuroscience and medical data science, working on identifing cell types, circuits and computations in the healthy and diseased visual system and improving clinical diagnostics. We are part of the Institute of Ophthalmic Research at the University of Tübingen and affiliated with the Center for Integrative Neuroscience and the Bernstein Center for Computational Neuroscience in Tübingen. Our official lab website can be found here.
A bit ago, we published a study in eLife mining a publically available electron microscopy dataset in an attempt to quantify the connectivity in the outer retina. We found that rod bipolar cells (which, as the names suggests, are thought to contact rods primarily) also contact cones, and quite frequently so. This was now confirmed independently by the lab of Sam Wu, in an article published in Journal of Comparative Neurology. They also show that these are likely active synaptic sites, as there is mGluR6 expressed there.
Our new paper in collaboration with the Euler lab has just been published by Current Biology. Camille recorded light-evoked Ca2+ signals in horizontal cell dendrites and showed that they reflect the cone opsin gradient. In contrast to the widespread hypothesis that horizontal cells are globally coupled, chromatic preferences in neighboring dendritic tips vary markedly, indicating that mouse horizontal cells process cone photoreceptor input locally. We contributed help in data analysis and our first ever multicompartment model based on a beautifully reconstructed entire dendritic branch of a horizontal cell.
The lab is part of an initiative that NIH will fund to build a BRAIN Initiative comprehensive cell type center to make an atlas of all the cell types in the mouse brain. We will collaborate with the Allen Institute for Brain Science, Baylor College of Medicine, Karolinska, Harvard, Caltech and others in this exciting project! Our team will be responsible for mapping RNAseq-data to physiology, which will provide many new interesting machine learning challenges.
Last week, a lab delegation was at the European Retina Meeting 2017 in Paris. It was a fun meeting, with a number of interesting talks and posters on a variety of topics. Two examples include the talk by Leon Lagnado (also on image) from Sussex who showed that one can infer the release of single vesicles from GluSnFr-experiments. Greg Field from Duke had an interesting talk about coding with DS cells at different light levels. Tübingen was represented strongly with more than 10 posters across labs. Looking forward to the next ERM 2019 in Helsinki and then some work to make ERM 2021 in Tübingen happen!
Cornelius and I visited Petri Ala-Laurila‘s labs at Alto University and University of Helsinki from 9-12th of August to discuss neural coding in the retina and potential collaborations. Thanks to our hosts! I am looking forward to ERM2019 in Helsinki!
We spent two intense days at Kloster Obermarchtal on a joint lab retreat with the labs of Thomas Euler and Katrin Franke to discuss where we are currently at with our projects, were we want to go and what we want to achieve. Tom Baden, Günther Zeck and Matthias Bethge came as guests to provide feedback and input and discuss collaborations. Also, Tom gave an entertaining talk about the latest on fish vision.
Thanks everyone for the commitment and the discussions!
Together with some people from the Euler lab we participated in the 100k relay race of the University of Tübingen. The race is special because you run in pairs and 1k at a time, ten times each. Effectively, that makes it ten 1k-sprints. We made a very good 11th place out of 37 teams!
This week, we have finally released the results of the spikefinder challenge to infer action potentials from calcium recordings. We had more than 50 submissions, many of them in the last few days of the challenge. Obviously, deep learning frameworks were hugely popular, but also “classical” generative modeling approaches (“MLspike”) did remarkably well. Here are the top 10:
We declared Patrick Mineault (Google), Nikolay Chenkov (BCCN Berlin), Peter Rupprecht and Stephan Gerhard (FMI Basel) joint winners, as there submissions were extremely close to each other. A lively debate emerged on twitter about what it all means:
— Philipp Berens (@CellTypist) 13. Mai 2017
Our preliminary analysis can be found on github. A more complete paper with thorough discussion and analysis will follow.
On occasion of the Meeting of the German Neuroscience Society, I received the FEI Technology Award 2017 for my work on using machine learning to define cell types in the nervous system.