Pachitariu + Stringer lab

Our lab is at HHMI Janelia Research Campus (near DC), a fully-funded non-profit research institution. Janelia just received a $500 million investment for AI research 🤖, more info here.

We are recruiting PhD students!

Research

Our lab combines machine learning / AI techniques and large-scale imaging to investigate plasticity rules and sensory representations in cortical circuits. Example recording of 50,000+ neurons simultaneously at 3Hz, using two-photon calcium imaging:

Learn more about our research here and see all publications here. We share all the data generated by our studies, linked here. We also have developed several data processing packages for the bio/neuro community: cellpose, kilosort, suite2p, facemap, and rastermap.

News

• Analysis methods for large-scale neuronal recordings review published!
• Cellpose development highlighted in a Nature technology feature!
• Rastermap paper is now out here! News coverage
• Congrats to Fengtong Du et al, preprint now out: Towards a simplified model of primary visual cortex!
• Kilosort4 paper is now out here!
• Congrats to Lin Zhong et al, preprint now out on Distinct streams for supervised and unsupervised learning in the visual cortex!
• Facemap was featured in a Nature Methods research highlight!
• Congrats to Atika Syeda et al for the publication of the Facemap paper!

Resources

• About HHMI Janelia Research Campus
• HHMI’s values
• HHMI’s commitment to Diversity, Equity, and Inclusion
• Being a postdoc at Janelia

Talks

• Rastermap tutorial
• Facemap tutorial
• Kilosort 4 talk
• Making sense of large-scale neural and behavioral data with Facemap and Rastermap talk
• Cellpose 2.0: how to train your own model talk, talk+tutorial
• Cellpose talk, talk+tutorial
• Suite2p talk
• Kilosort 1, 2, 2.5 & 3 talk
• High precision coding in visual cortex short talk, long talk
• High-dimensional geometry of population responses in visual cortex talk
• High-dimensional problems in neuroscience talk
• Spontaneous behaviors drive multidimensional, brainwide activity talk

Media Coverage

• Novel visualization method helps make sense of large neuronal activity datasets, Medical Xpress

• New tool helps scientists spot patterns in mountains of data, Howard Huges Medical Institute

• Six tips for going public with your lab’s software, Nature

• Janelia scientists release state-of-the-art spike-sorting software Kilosort4, Howard Hughes Medical Institute

• Predicting neural activity from facial expressions, Nature Methods

• Tiny faces, big expressions: Reading rodent faces, Penn NeuroKnow

• Reading the mouse mind from its face: New tool decodes neural activity using facial movements, Howard Hughes Medical Institute

• Noisy solo neurons show consistency in groups, Howard Hughes Medical Institute

• High precision coding: How the visual cortex processes information about the world, Scientifica

• New tool maps boundaries of diverse cells in microscope images, Howard Hughes Medical Institute

• Python power-up: new image tool visualizes complex data, Nature

• A Power Law Keeps the Brain’s Perceptions Balanced, Quanta magazine

• Power Law Discovery May Explain Why You Can See the Forest and the Trees, Simons Foundation

• ‘Noise’ in the Brain Encodes Surprisingly Important Signals, Quanta magazine

• Thinking on the Go: Why Does the Whole Brain Light Up for Just the Smallest Movements?, Simons Foundation

• profile + podcast, Stories of Women in Neuroscience (WIN) by Daniela Cassataro

• Understanding 40,000 neurons, Brain Inspired podcast by Paul Middlebrooks

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