Representing all authors, Katrin and I received the paper of the year award for a paper in the basic sciences from the medical faculty of the University of Tübingen 2016 for our paper “The functional diversity of mouse retinal ganglion cells“, awarded by Thomas Gasser, the vice-dean of the medical faculty.
Postdoctoral Researcher (TV-L E13 100%)
Medical Data Science for Ophthalmology
to be filled as soon as possible, with funding for up to 4 years.
I have been considering this for a while, here is one new year’s resolutions for 2017: Moving beyond Frontiers. There’s lots of evidence that we should not take Frontiers seriously (anymore?) as a scientific publisher.
Calcium imaging is one of the most widely used techniques to acquire data from large populations of neurons. Unfortunately, inferring action potentials from the measured calcium traces is not straightforward and algorithmically far from solved.
To make progress in this direction, we opened the spikefinder challenge at http://spikefinder.codeneuro.org/!
We collected a large dataset of simultaneous two-photon imaging and electrophysiologically records and made it available separated into training and test sets. We ask you to design your favorite algorithm and submit your results on the website!
What is your benefit?
- You get to advance the community
- All algorithms that beat state of the art will be included in an overview paper and you will be coauthor
- The top three teams will win a 1200/500/300 EUR award sponsored by our partner ZEISS AG.
We look forward from receiving your submissions. The deadline is the 31st of March 2017.
You might also be interested in the neurofinder challenge at http://neurofinder.codeneuro.org/ – a challenge to find the best ROI detection algorithm.
Philipp, Jeremy, Matthias, Andreas, Josh, Lucas
The first paper from my lab “Connectivity map of bipolar cells and photoreceptors in the mouse retina” has just been published by eLife. Congratulations to Christian for his first paper as well!
Together with Timm Schubert from Thomas Euler’s lab we reconstructed the photoreceptors in a publicly available EM dataset of retinal tissue. We build on the work of Moritz Helmstaedter and colleagues, who made their entire dataset and code available – to me this is a great example of how open science can fuel discovery. Our code and data can be found here. The project was our first adventure in connectomics, which provided a great learning experience for everybody involved.
Our collaborative research center “Robust Vision – Inference Principles and Neural Mechanisms” got approved by the German Research Foundation on Friday! This is great news – together with a great team of >20 PIs, we will tackle the question why biological visual systems show so remarkable robustness building on our joint expertise in experimental and computational neuroscience, machine learning and computer vision.
Last year, we published our study “Principles of connectivity among morphologically defined cell types in adult neocortex” in Science. The paper generated quite a bit of attention – and now a technical comment, which was recently published in Science. In their comment, Barth et al. criticize our study as (i) overstating the completeness of our study; (ii) reporting a potentially biased connectivity matrix due to technical limitations of our brain-slicing and multipatching methods; and (iii) simply renaming previously identified interneuron types.
Details of our reply to their criticism can be found in the published version. In particular, we addressed their point about potential biases in the connectivity matrix due to slice cutting quantitatively. Assuming that the neuron are approximately rotationally symmetric, we computed the amount of overlap of their dendritic and axonal fields potentially cut away by the slicing (because this is were connections between the two can happen). A similar method had been used before by Levy and Reyes. The analysis clearly shows that the correction factor that needs to be applied does not strongly depend on the cell type pair, suggesting that the connectivity matrix may need to be scaled, but is unlikely to be distorted.
In the course of preparing the reply, we also submitted all fully reconstructed neurons from that study (n=298) to neuromorpho.org, where they will be available shortly.
Starting July 1st, we are part of the Institute of Ophthalmic Research at the University of Tübingen. The institute aims at uncovering the causes of diseases of the eye and develop treatments based on these discoveries. To our basic science research, we will therefore add a clinical component, which I am very excited about. The IOR wrote a short news report about our start, which you can read here. My group will be mainly funded by the Bernstein Award of the German Ministry of Science and Education. We will remain affiliated with the Center for Integrative Neuroscience and the Bernstein Center for Computational Neuroscience in Tübingen.
Our new phone number is: +49-7071-2988833
Finally, our paper on “Benchmarking Spike Rate Inference in Population Calcium Imaging” has been published – as a NeuroResource in Neuron. In the paper, we evaluate a range of algorithms for spike rate inference from calcium imaging data on a large ground-truth dataset. What’s important is that the recordings were all performed under realistic conditions for population imaging, that is without zooming in on individual cells. This makes the task much more difficult – the best algorithms achieve correlations of 0.5-0.6 when evaluated in time bins of 40 ms. It will be interesting to find out whether this can be improved upon by better algorithms or whether new indicators and imaging systems are needed for that. We provide our method, which performs very well under a wide range of recording conditions, for ready reuse.