A seminar held by the researchers of the Allen Institute for Brain Science

Monday, 6 June, 2022

The brain is the most complex of all biological systems, and we still know very little about how it works. To change this, the Allen Institute's studies and programs means significant help, and they are teaching us how.

Founded in 2003, the Allen Institute for Brain Science, based in Seattle, Washington, is the oldest scientific unit of the Allen Institute. Its goal is to identify and characterize the cell types and connections that make up our brains. This is necessary because, despite all the sensational discoveries, we still know very little about the brain. We know about the connections between neurons, but not much about how our brains process information. We have Nobel Prize-worthy insights into how memory is formed, but we have no explanation for why people learn faster, concentrate better than others, or are more creative. All this is surely linked to a phenomenon called synaptic plasticity, but how?

There are many unanswered questions, and to answer them we need to understand brain cell types, how they are interconnected, and how they change during natural aging and in neurodegenerative diseases such as Alzheimer's.
Not only is it not easy to carry out this huge task, but it is also not easy to plan the subtasks to be solved. Today, when we often encounter databases in our daily lives, it seems natural that carrying out subtasks also means creating databases - even if the number of such data files is something that only astronomers take for granted. The institute has already created a number of core data resources for the neuroscience community by sharing the results of their studies of the brain at the level of gene expression, connectivity, and individual cell types or synapses.

AIBS researchers are currently using electron microscopy to create a 3D map of the brain's "microconnectome", a realistic representation of how neurons are connected. The scale of the task is illustrated by the following data: there are about a billion synapses (nerve connections) in a cubic millimeter piece of the mouse brain, about the size of a grain of sand.

This work, and more importantly its usability and applicability, will be the subject of a one-day workshop - lectures and exercises - at our institute by three colleagues from the Allen Institute for Brain Science, one of whom is our former Ph.D. student and later colleague Ágnes Bodor. Because you can find not only Hungarians in all the important places in the world but also good people from our institute.

If you want to see realistic neurons in 3D, you can visit the MICrONS Explorer program page on the institute's website!

The program of the event

June 2 Thursday (Institute of Experimental Medicine)
3D EM "MICroNS workshop"

8.30-9 .00 Covid antigen testing

9.00-9.30 Brief introduction to the datasets Nuno da Costa & Forrest Collman
9.30-10.10 The cellular and synaptic organization of a cortical column in mouse visual cortex Nuno da Costa

10.10-10.20 Break

10.20-10.50 Local and long-range connectivity of L5 thick tufted cells
Agnes Bodor
10.50-11.40 Quantitative census of local somatic features in mouse visual cortex Forrest Collman
11.40-12.30 Lunch

12:30 – 13:00 Introduction to tools (breakout into 3 groups)
Forrest Collman, Agnes Bodor, Nuno da Costa

13.00 -17.00 Hands-on in 3 groups. Participants will work on their chosen mini-projects. Using one or more sets of tools.

- using a web browser interface to study the dataset Agnes Bodor
- query connectivity data through a browser-based user interface application Nuno da Costa
- to query the data via a python API Forrest Collman


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