How many brain cell types are there? What is their form, function, and how do they connect? Teams at the Allen Institute for Brain Science are working to answer these foundational neuroscience questions. By cataloguing and genetically profiling cell types of the brain with incredible precision and detail, we are working to improve our fundamental understanding of brain development, evolution, and disease.
This webinar series covers the ins and outs of the Allen Institute’s open data and cell type taxonomy tools. Missed a session or want to revisit the material? Browse all recordings below.
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Previous Webinars
Spatial Transcriptomics: How Team Science Created the ABC Atlas | Oct 30, 2024
Description
This webinar will focus on how the Allen Institute uses team science to tackle large-scale projects. We will focus on the teams involved in our spatial transcriptomics pipeline and the journey that cells take, all the way from our histology lab to being featured online in tools such as the ABC Atlas.
Time
9-10am PST
MapMySpikes Data Challenge | Nov 20, 2024
Description
This webinar will feature an introduction to our previous data challenge MapMySpikes, where participants were challenged to map cell types onto Allen Institute transcriptomic taxonomies using electrophysiological data, and a talk given by our data challenge winner featuring their winning tool.
Time
9:30-10:30am PST
The Annotation Comparison Explorer | Dec 18, 2024
Description
This webinar will focus on the Annotation Comparison Explorer (ACE), a new tool for comparing annotations across Allen Institute transcriptomic taxonomies. This tool can also be used to compare annotations across transcriptomic cell types from Alzheimer’s Disease studies as well.
Time
9:30-10:30am PST
All About Single Cell/Nucleus Transcriptomics | Jan 22, 2025
Description
This webinar will be an introduction to single cell transcriptomics, how this technique is used at the Allen Institute, and how “single cell” transcriptomics compares to “single nucleus”.
Time
9:30-10:30am PST
The Seattle Alzheimer's Disease Brain Cell Atlas | Feb 12, 2025
Description
This webinar will focus on The Seattle Alzheimer’s Disease Brain Cell Atlas (SEA-AD), featuring some of the scientists behind the project. The goal of the SEA-AD Atlas is to characterize the cellular and molecular changes that occur during the progression of Alzheimer’s disease, using single nucleus– and spatial transcriptomics and other techniques.
Time
9-10am PST
Programmatic Access to ABC Atlas Data | March 26, 2025
Description
This webinar will focus on using Allen Institute Jupyter notebooks to access datasets featured in the ABC Atlas, such as the whole mouse brain single cell transcriptomics dataset.
Time
9:30-10:30am PST
Transcriptomic Cell Type Changes in the Aging Brain | April 23, 2025
Description
This webinar will focus on a recent scRNAseq aging mouse brain study from the Allen Institute (Jin et al., 2025) and how to access these data in the Allen Brain Cell (ABC) Atlas.
OFFICE HOUR: Single cell/nucleus RNAseq Office Hour | May 7, 2025
Description
For this virtual office hour, we will have Emma Thomas and Aaron Garcia available to answer questions related to single cell/nucleus RNA sequencing. Emma is a Scientist II on the Molecular Genetics Team, where she focuses on the generation and analysis of 10x single-cell and single-nucleus RNA-seq data across the whole mouse brain. Aaron is a Scientist I on the Human Cell Types Team, where he focuses on generating 10x multiome data from human and NHP tissues for BICAN taxonomies. Please submit your questions in advance through the registration link; we will also answer questions live if time permits.
OFFICE HOUR: Clustering/Taxonomy Building Office Hour | May 20, 2025
Description
For this virtual office hour, we will have Nelson Johansen and Dan Yuan available to answer questions related to clustering transcriptomic data and building taxonomies. Nelson is a Scientist II on the Human Cell Types Team, where he focuses on cross-species BICAN taxonomies and comparative analysis. Dan is a Scientist I on the Informatics and Data Science Team, where she focuses on human aspects of cross-species BICAN taxonomies. Please submit your questions in advance through the registration link; we will also answer questions live if time permits.
OFFICE HOUR: New Features in the Allen Brain Cell (ABC) Atlas | August 13, 2025
Description
For this virtual office hour, we will have Elysha Fiabane and Rachel Hostetler available to answer questions related to new features and datasets in the ABC Atlas. Elysha is a Product Manager on the Data & Technology team, where she oversees the design and development of web products like the ABC Atlas. Rachel is a Scientist I on the Human Cell Types Team, where she provides technical support, training, and outreach to users of Allen Institute tools and datasets.
Time
10 - 11 AM PST
MapMySections Data Challenge Winners | August 27, 2025
Description
This webinar will feature a brief introduction to our MapMySections Data challenge, where participants were challenged to map serial two-photon tomography images from the Genetic Tools Atlas to spatial transcriptomic cell types in the ABC Atlas, followed by presentations by the data challenge winners.
Time
10 - 11 am PST
Additional Webinars
Cell Types 101
This webinar will feature an introduction to the study of cell types! We will cover evolving cell type definitions, cell types across species, the types of data used to define cell types, and the importance of having standard definitions for cell types. This will be a great starting point for those who are new to cell types, and refresher for the experts.
Recording of this webinar is available on our YouTube channel here.
What is a taxonomy?
This webinar will focus on the systematic classification of cell types and their hierarchical relationships. Much like species taxonomy (family, genus, species, etc.), researchers at the Allen Institute and their collaborators are working to create a standard taxonomy for cell types.
Recording of this webinar is available on our YouTube channel here
PatchSeq: The techniques behind the Cell Type Knowledge Explorer
This webinar will focus on the Cell Type Knowledge Explorer, a cell type taxonomy tool created by the Allen Institute and their collaborators. Here we will learn how transcriptomic, morphological, and electrophysiological data is generated and used to define cell types in the CTKE.
Recording of this webinar is available on our YouTube channel here.
Cross-species cell types
This webinar will also focus on the Cell Type Knowledge Explorer, a cell type taxonomy tool created by the Allen Institute and their collaborators. Here we will learn how multimodal data is used in the CTKE to determine cell type homologies across species (mouse, human, and marmoset) in the primary motor cortex.
Recording of this webinar is available on our YouTube channel here.
What is your cell type: MapMyCells
This webinar will focus on MapMyCells, a new interactive cell type taxonomy tool. MapMyCells allows for users to upload their own cell type data and compare it to taxonomy datasets generated by the Allen Institute and their collaborators.
Recording of this webinar is available on our YouTube channel here
Introduction to ABC Atlas
This webinar will focus on the Allen Brain Cell (ABC) Atlas, a platform for visualizing single cell transcriptomic data in the brain. Currently, the atlas features spatial, non-spatial, human, and mouse data; this webinar will be an introduction to and a general overview of the atlas.
Recording of this webinar is available on our YouTube channel here
This webinar series was supported by the National Institute of Neurological Disorders and Stroke of the National Institutes of Health under Award Number U24NS133077. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
This series is over! Recordings and descriptions are listed on this page and also can be found on our Allen Institute YouTube channel.
