Open for (neuro)science: Pre-symposium tutorials

Leading up to the Open for (neuro)science symposium and tutorials on March 8-10, 2021, join us for additional tutorials showcasing more open resources from the Allen Brain Map. At these tutorials, learn how and why to integrate these open resources into your research.

The tutorials do not assume any prior experience with the open Allen Institute for Brain Science resource being covered. Certain tutorials may assume prior Python experience, as noted.

Symposium information

New from the Allen Cell Types Database: Patch-seq and synaptic physiology

February 24, 2021 | 10:00-11:00am PT

The goal of the Allen Cell Types Database is to characterize all cell types in the human and mouse brain, their properties, and their interactions. These two new resources from the research capture multimodal morphology, electrophysiology, and transcriptomic data from the same cells (patch-seq) and electrophysiological recordings of groups of neurons interacting (synaptic physiology).

The patch-seq dataset includes data from mouse and human experiments recording electrophysiological, transcriptomic, and morphological data from individual neurons. The dataset provides a foundation for reconciling transcriptomic and morpho-electric cell types developed as part of the Allen Cell Types Database goal of producing a complete taxonomy of cell types in the human and mouse brains.

The synaptic physiology dataset includes simultaneous in vitro patch clamp physiology of groups of neurons in the mouse primary visual cortex and human middle temporal gyrus. The dataset provides insight into connection probabilities, synaptic strength, and short-term plasticity related to the goal of identifying neuronal function across cell types and brain regions.

Python experience recommended.



Tools for modeling: The Brain Modeling Toolkit and SONATA data format

January 28, 2021 | 10:00-11:00am PT

The Brain Modeling Toolkit is a Python-based open software package for building, simulating, and analyzing large-scale neural network models. It supports the building and simulation of models at various scales.

The Brain Modeling Toolkit is linked to SONATA, a standardized data format for storing networks and simulations. These software tools together support the development and sharing of neural networks, simulations, and other modeling findings.

Python experience strongly recommended.



Get oriented to

December 9, 2020 | 10:00-11:00am PT

The Allen Institute for Brain Science has been sharing all of our data openly since the introduction of the Allen Mouse Brain Atlas in 2004.

We now have more than a dozen open databases, as well as data analysis tools, biological lab resources, and more. This tutorial will give a brief introduction to the breadth of resources available and take questions from the audience to help identify which ones are the best fit for various uses and needs.



Atlases for development: Brainspan Atlas of the Developing Human Brain and Allen Developing Mouse Brain Atlas

November 19, 2020 | 10:00-11:00am PT

Our whole-brain gene expression atlases are our most popular resources. These two resources provide gene expression data on the developing mouse and human brain.

The Allen Developing Mouse Brain Atlas three-dimensional map of gene expression throughout the mouse brain at seven stages of development, containing information on 2000 genes selected for their relevance to development. It comprises cellular resolution in situ hybridization images with comprehensive coverage that reveal where each gene is expressed in the developing mouse brain, as well as corresponding age-matched anatomical reference atlases.

The Brainspan Atlas of the Developing Human Brain maps gene expression across the developing human brain. It includes RNA sequencing and cellular-resolution in situ hybridization across selected brain regions, microarray transcriptional profiles across the whole brain, and corresponding anatomical reference atlases at multiple points of development.