I think the hippocampal formation is one of the hardest regions to understand with regard to its overall shape and connection patterns. In the rodent it crosses all three axes in the brain and the orientation of its convoluted layers changes across its septal-temporal axis. Therefore, I am happy to share with you a video that I produced recently, in which I show how the hippocampal formation looks like in 3d. For me it was also a good exercise to produce a video for Youtube, as I am going to produce more in the next weeks.

This video is fascinating and frustrating (from a computational modeling point of view) at the same time. Jeff Lichtman shows in this video (above) the complexity of a tiny little fraction of the mouse brain scanned on a nanometer scale using serial electron microscopy. At 16:00 and the following minutes he shows the relation between the nanometer scale, the complexity that can be observed on this level and the large scale view on the brain. Absolutely impressive.

Functional connectivity of the entorhinal-hippocampal space circuit by Sheng-Jia Zhang and colleagues from the Kavli Institute for Systems Neuroscience in Trondheim.

They used light-evoked discharges of grid- and other cells to determine whether these cells have direct hippocampal projections. What I find interesting about this study is that principle cells in MEC need between <5-30ms to fire, depending on the current they receive.

New and Distinct Hippocampal Place Codes Are Generated in a New Environment during Septal Inactivation by Mark Brandon and colleagues from the Center for Functional Connectomics in Seoul.

In this paper they show that septal inactivation leads to reduced theta power and grid cell activity. In a novel environment place fields emerged which suggests (according to their interpretation) that neurons can generate place fields without grid cell activity.

The Allen Brain Atlas provides most of their tracked brain data as 3d-files in the VTK-format. I found it difficult to find a converter for this format that would give me e.g. an obj-file. I came across the Graph Toolbox for Matlab which can read vtk-files and write obj-files. However, their importer did not work for that particular version of the vtk-format. Here is read_Allen_vtk.m, an m-file that I derived from read_vtk.m, which is able to extract all vertices and face-data from the vtk-files. You can then save them using write_obj() and open them in the 3d-tool of your choice. In the  upper image you see the hippocampus and entorhinal cortex of the mouse in Blender.

Recently, I had a bunch of images for which I wanted to make all grey pixels transparent, in order to just see the color coded regions.

This was one of the situations, in which I was wondering whether I should do it manually (for 37 images) with Gimp, or write a script that can do the job for me. I was happy, that I decided to write a script, because it turned out that it just took me one minute to figure out the commands in Matlab and an additional minute to write the script. At the end I saved a lot of time and obtained images with an even more accurate mask than those images that I produced with Gimp. Here is the script for this kind of job:


function maskImage(filename)
a = imread(filename);
c = ((a(:,:,1) == a(:,:,2)).* (a(:,:,2) == a(:,:,3))) == 0;
imwrite(a, filename, 'png', 'Alpha', double(c));

Molecular Movies is a collection of animations of molecular and cell reactions. I stumbled upon this side when I was looking for 3d depictions of the hippocampus. A very nice animation by Drew Berry can be found here and here on Youtube.