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Join us for a hands-on opportunity to learn how to use volumetric electron microscopy (EM) data and address biological questions central to the thalamus and striatum at the Emerging Connectomics of the Thalamus and Striatum Workshop, hosted at by the Allen Institute. This in-person workshop will take place between May 6 and May 7, 2026 in Seattle.
Allen Institute, Seattle, WA
Audience
Graduate, Postdocs, Scientists
Workshop Topics
Workshop Goals
This workshop is geared towards both participants with an interest in learning how to use EM data to address biological questions, and participants interested in using and developing computational methods for data discovery. Ideally the workshop will be a blend of participants with different levels of biological and computational expertise. No coding experience required to apply.
Datasets
Two new EM volumes covering much of the MD thalamus and striatum are being produced now and will soon be ready to use to map neural circuits with synaptic resolution. These datasets bring new opportunities and challenges in both biology and data analysis. This workshop will bring scientists from diverse backgrounds together to engage with these datasets at an early stage in order to accelerate discovery and enrich our understanding of the anatomy, cell type diversity and connectivity of these brain regions.
PVT and MD Thalamus volume
EM volume with dimensions of 0.5 mm (medial-lateral), 0.5 mm (rostral-caudal) and 0.5 mm (dorso-ventral). The dataset contains APEX/HRP labels (Zhang 2019) targeted to the incoming axons from medial prefrontal cortex, ventral endopiriform nucleus, and ventral pallidum, and the soma of MD/PVT cells projecting to prefrontal and orbito cortex .
Zhang Q, Lee WA, Paul DL, Ginty DD. Multiplexed peroxidase-based electron microscopy labeling enables simultaneous visualization of multiple cell types. Nat Neurosci. 2019 May;22(5):828-839. doi: 10.1038/s41593-019-0358- 7.
Dorsal-Medial Striatum volume
EM volume with dimensions of 1 mm x 0.5 mm x 0.5 mm. The EM dataset contains APEX/HRP labels targeted to the incoming axons from medial prefrontal cortex, Amygdala and VTA; and the soma of D1 and D2 medium spiny neurons in the striatum with the facilitation of enhancers (Hunker 2025).
Hunker AC, Wirthlin ME, Gill G,…Ting JT. Enhancer AAV toolbox for accessing and perturbing striatal cell types and circuits. Neuron. 2025 May; Volume 113, Issue 10, 21: 1507-1524.e17. doi: 10.1016/j.neuron.2025.04.035.
Travel Funding
There is no fee to participate in the workshop. There are limited availability of travel funds to assist in domestic travel and accommodations. Please indicate on the application if there is a need for travel support. Note that we cannot reimburse travel expenses incurred independently and applicants receiving travel support must book through the Allen Institute’s travel agent.
Grant & collaboration acknowledgements
This workshop is generously funded by the BRAIN Initiative through the CONNECTS program through the National Institute of Neurological Disorders and Stroke (NINDS) of the National Institutes of Health under the Award number UM1NS132253. The thalamus dataset is being generated by the Allen Institute while the striatum dataset is being generated at Princeton.
Oct 20, 2025
Sep 16, 2025
Sep 15, 2025
Nov 15 - 19, 2025
