Category Archives: Electron Microscopy

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

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 ( 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 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

Comparative Connectomics paper is out!

papertitleFinally, after years of blood sweat and tears our comparative connectomics paper has been published. This represents a huge victory for myself and all of the people who have helped me along the way. It is rather humbling to have this work get the kind of exposure it gets by being published in Cell. It is the culmination of years of work, complete with with heart-breaking failures, long grinding hours on the microscope and in front  of the computer, and the occasional adrenaline-inducing discovery. In the paper, we compare a wiring diagram(or connectome) of the pharyngeal nervous system of the nematode Pristionchus pacificus to that of the well-known model organism C. elegans. The data are obtained by Continue reading

Faces in the worm.

2975_Montage Acquisition0001Reconstructing neurons from thousands of images is typically a very dull, repetitive and labor intensive task. Some would say that the long periods of monotony, broken by occasional excitement caused by an unexpected discovery, is enough to drive you insane. Yet it is how I spent much of my time. Either because I have gone crazy or more likely out of a need to amuse myself with the task I have started to notice faces in the micrographs. This is not all that surprising really. As humans we are really pre-programmed to recognize anything that has the same proportions as a face… all we need are two dots for eyes  something that looks like a mouth in the right places. As mitochondria are typically tube shaped they can very easily substitute for a mouth or a pair of eyes in an image, so most of them time these are what construct the features of the face. Sometimes, the inner membranes of the mitochondria even stain in such a way as to resemble teeth in the mouth! Perhaps it is a reflection of optimism that the vast majority of faces that I notice are smiley faces. For anyone that is amused, I’ve started collecting them and have uploaded them to a Flickr gallery. Click HERE for the link! expert review

eyewireIt is not so often that some piece of software comes out that gets me as excited as what the folks at are doing. What they are attempting to do is to take one of the most difficult aspects of generating synapse-level “Connectomes” and speed it up by crowd sourcing the labor. By breaking the task into pieces that can be completed in short periods of time and adding some game-like elements, they hope they can dramatically speed up their reconstructions of the human retina connectome. But how useful is it really? Continue reading