Category Archives: Connectome

Jeff Lichtmann TED talk

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.

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Talk at Institute of Molecular Pathology, Vienna

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On Wednesday I was at the IMP in vienna to deliver a talk about my recent paper.Manuel Zimmer, my host, put together a great schedule of people to meet with and I had a great time delivering the talk .. the audience was highly engaged and asked a lot of very good questions. I spent the rest of the day having some great discussions with members of top-notch labs Continue reading

Räuberischer Schlund

predatorypressreleaseMuch to my amusement, I found out that the local newspaper, the Schwäbisches Tagblatt, picked up on our press release and published a nice little story. The title “Räubuerischer Schlund” translates to “Predatory Mouth”, referring to  the toothy mouth Pristionchus pacificus uses to puncture its prey. Pretty cool! The image on this post is the same one used in the press release, and shows P. pacificus chomping down on C. elegans. Click HERE for a link to the article. It’s in German, so if you need to you can have a look at it in google translate.

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

Pristionchus pacificus predatory feeding video

One of the things that interests me about the nematode Pristionchus pacificus is that it is capable of taking advantage of many different food sources. Like it’s cousin and well known model organism Caenorhabditis elegans, this nematode can be raised on agar plates seeded with bacteria. Pristionchus can additionally feed on other sources, including other nematodes! These predatory feeding behaviors are quite distinct from bacterial feeding. For instance, Pristionchus has tooth-like denticles in its mouth opening that are highly active during predatory but not bacterial feeding. This increase in the complexity of the P. pacificus
behavioral palette is most interesting when you consider that the nervous systems are composed of a nearly identical set of neurons. So how do you teach an old nervous system to do new tricks? This is one of my primary motivations for comparing networks of synaptic connectivity between these two species.

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!

Eyewire.org expert review

eyewireIt is not so often that some piece of software comes out that gets me as excited as what the folks at eyewire.org 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