WormID.org
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Code, apps, and reference datasets for neuronal segmentation, identification, and time-series quantification of whole-brain imaging experiments in C. elegans.
The Innovation Core at the Weill Institute
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A facility in Mission Bay, San Francisco providing the use of a variety of cutting-edge commercial and bleeding-edge development-stage microscopes, training, support, and demos for both UCSF and outside scientists.
Course: Encoder-Decoder Models for Neuroscience
NS219 UCSF Spring 2026 course page
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Many machine learning approaches can be thought of as a process of encoding high-dimensional data items into a low-dimensional space, then (optionally) decoding them back into a high-dimensional data space. This paradigm encompasses the endeavors of dimensionality reduction, feature learning, classification, and of particular recent excitement, generative models. Encoder-decoder models have also been proposed as an architecture of human cognition. This course surveys uses of encoder-decoder models in current neuroscience research and teaches the basic theory and practice of applying these models.
CLEF (Closed-Loop Experimental Framework)
A Python software framework to facilitate structured, scale-ready development of closed-loop experiments. Used by our lab and several others. Contact us for access.