Category Archives: Connectome

Journal Club: Connectomic reconstruction of the inner plexiform layer in the mouse Retina

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 Continue reading

My thoughts on the first BRAIN initiative meeting

cropped-Gogli1The 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

The Connectome Blog and Scientific Community

Connectome-Masthead“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

Getting the message out in the good old U.S.A.

WP_20130321_003Just 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

An artistic contribution to worm neuroanatomy.

sideview4Bumbargercover1In 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!

Data is online at Open Connectome

brainsectionWhen 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

Journal Club: Connecting a Connectome to Behavior

0yks_X4B3uHScKQYMpmLDzl72eJkfbmt4t8yenImKBVaiQDB_Rd1H6kmuBWtceBJAn 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