I was not satisfied with the available abstract depictions of the hippocampal formation and I didn’t want to worry about copyrights or citation obligations when I use them in scientific publications and presentations. Therefore, I thought it would be a great if there would be a free template figure in vector format that everybody can use, improve and share with others. Luckily, master student Stefanie Bothe, who makes an internship in our lab right now, created exactly this:

Screenshot from 2015-05-21 15:01:06

I opened a repository, called NeuroSVG, where you can download this figure and send pull request, if you would like to improve it. For your own usage, you can modify this figure and use it freely wherever you like. Maybe, others like to contribute further neuroscientific illustrations in SVG format in this repository.

Size of the rat hippocampus

Recently, I was wondering how long the rat hippocampus on the septal-temporal axis actually is. With my 3d model of the rat hippocampus and the Measure Panel Addon for Blender this is easy to measure. Simply select an edge loop within one of the planes and compute the path length.

Screenshot from 2015-05-20 11:26:07

I was pretty surprised when I saw that the dentate gyrus in my model is about 9.7mm long! First, I couldn’t believe that but when I looked into the original data by Kjonigsen et al. 2011, it became clear that this seems to be really the length of the rat hippocampus when it is unfolded in 2D.

Screenshot from 2015-05-20 11:30:53


Given the thin unmyelinated fibers in CA3 which have pretty long conduction times, signal processing within the hippocampal loop suddenly appears to be very slow. 😉

Visualization of traveling theta waves

Recent reports have shown that theta oscillations are in fact traveling waves along the septo-temporal axis of the hippocampus (at least in rats).

Lubenov and Siapas, 2009, Hippocampal theta oscillations are travelling waves

Patel et al., 2012, Traveling Theta Waves along the Entire Septotemporal Axis of the Hippocampus

Here is a little animation based on my 3d model of the rat hippocampus to show how the traveling waves might look like in CA1.

Projections from CA1 to Entorhinal Cortex

Screenshot from 2014-10-27 13:35:00I am currently modeling the projections from CA1 and Subiculum to Entorhinal Cortex using PAM. In the 3D-model, it is not so obvious how they should look like. The best, I could find is the collection of tracer studies that is available at the Allen Brain Atlas. For over 1000 injection sites you can analyse where in 3d-space the projections of the neurons are. In the example above you see, how CA1 neurons (green dot) project to the Entorhinal cortex (red cross). The green trace connecting the dot with the cross is almost invisible.

How to print 54 rat hippocampus models in one week?


Recently, we had the Memory and Mind workshop of the European Cluster of Excellence in our lab. On short notice, the organizers of this workshop approached me to ask whether I could organize 54 3d-printed models of the rat hippocampus for the participants. The models need to be printed within the next 7 days in order to give them to the participants.

It turned out, that most 3d printing services (and we needed one with selective laser sintering) simply cannot deliver within such a short time. Fortunately, I found trinckle, a startup in Berlin, who managed to produce and deliver 54 models of the rat hippocampus right on time to hand them out to the participants of the workshop at the last day. They now published a nice posting about the hippocampus and the 3d-model (in German).  Thank you!