Long time friend and fellow Sommer Lab postdoc just had a great paper come out in the most recent issue of Cell. Though I didn’t contribute anything intellectually to the paper, I was able at least to help them out with a couple images for Figure 1. I think the paper is a good demonstration of why one shouldn’t be afraid of working with non-standard model organisms.
Erik (along with Manuela Müller and Christian Rödelsperger, also in the lab) explores the mechanisms by which developmental plasticity Continue reading
In a landmark paper demonstrating the capabilities of modern connectomics approaches, Moritz Helmstaedter et al. present a reconstruction of nearly 1000 cells and 500,000 cell-cell contacts in the mouse Retina using data collected with serial block face microscopy. This is a high-throughput electron microscopy method championed by Moritz and two of the other co-authors, Kevin Briggman (now at NIH in Bethesda) and of course Winfried Denk (a Max Planck Director with joint appointment at Janelia Farm). Valuable in its own right, this paper represents
One of the groups in our lab, headed up by postdoc Erik Ragsdale, is investigating the genetics and evolution of a feeding polyphenism in Pristionchus. They just had a nice paper come out in Evolution & Development entitled: “Feeding plasticity in the nematode Pristionchus pacificus is influenced by sex and social context and is linked to developmental speed.” Once it was accepted, they asked me to help design a cover submission. I used some still captures from some of my predatory feeding movies, and the cover was accepted! Score another point for my artistic career! Check out the paper, and expect more cool work from this group on the same polyphenism to be coming out later this year.
The first of a series of planning meetings for the BRAIN initiative took place early this week in Arlington, VA. Officially called the NSF Workshop on the Physical Principles of Brain Structure and Function, it collected many of the nation’s most prominent neuroscientists together into a stuffy hotel conference room to Continue reading
“Connectomics” is a nascent but growing discipline. As evidence of this, a simple pubmed search of Connectome will show that at the end of 2010 there were fewer than 20 papers using the word. It’s growth seems to be exponential, however, as today the same search yields nearly 200 hits. One of the artifacts of being an emerging discipline is that there is very little established infrastructure for promoting community between all of the various participants in the field. Probably the most prominent Continue reading
Just got back from a whirlwind tour of the greater Washington D.C. area, where I was given my opportunity to present my work at two different institutions. My first stop was Janelia Farm, a Howard Hughes institute and one of the major drivers that are pushing the electron microscopy and computational technologies needed for large scale synapse-level connectomics work. I was invited by Albert Cardona Continue reading
In annotating all of the connectivity for my recent comparative connectomics papers, one of the byproducts was a massive 3D model of the anatomy of all the cells in the nervous system. For me, these models are fascinating to look at and I enjoy when I get a chance to admire some of the beauty in the data I generate. I spent some time making some 3D rendering of the models using Blender (www.blender.org) in order to submit them as possible covers for the issue in which the paper was published… they weren’t chosen for the cover, but I still want to share them with the world! Click the images to see them larger on my FLICKR page, and let me know what you think!
When image stacks are acquired for generating connectivity datasets, there is so much information in the micrographs that does not make it into the first manuscript. As these datasets are extremely difficult to acquire, I think it is important that we try and make the data as openly available as possible. This, however, is not an easy task… it requires you to spend quite a bit of time developing a resource… time that could be spent generating more data or writing papers. As such, I am terribly thankful that the folks at openconnecto.me have developed a resource for making easy for people such as myself to host their image data in a useful way. Right now, one of the Continue reading
An obvious goal of connectomics is to use it is a tool for better understanding complex network function. As new data are becoming available it is not entirely clear what the best methods are for extracting useful information out of connectivity matrices. Part of the problem lies in the fact that while a wiring diagram is necessary for understanding nervous system function, it is hardly sufficient. The painful reality is that in complex systems like networks of neurons, small details of neuron and synapse function can dramatically alter system behavior. A recent Plos Computational Biology paper by Eduardo Izquierdo and Randall Beer at Indiana University makes what I think is a useful contribution to the problem by Continue reading
Jeff Lichtmann just did a TED talk at connetomics at Caltech that is really worth a watch if you are interested in Connectomics. A couple of weeks ago he gave a longer version of the same talk here at the MPI in Tübingen. I think it does a fantastic job of defining why someone would be interested in “Connectomics”, presents an honest depiction of the magnitude of some of the technological problems involved, and, for me at least, leaves you with some hope that we can make big things happen by pursuing this approach. Something that comes across better in person than on YouTube are these amazing reconstructions where they have gone so far as annotate the positions of all of the synaptic vesicles. Strikingly beautiful! Nicely done talk that will get a lot of exposure, and I hope that it inspires more people to be doing this kind of work.