Pachitariu + Stringer lab

Our lab is at HHMI Janelia Research Campus (near DC), a fully-funded non-profit research institution.

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

• Check out our lab’s SfN posters:
  • Nov 17 PM Q2: PSTR224.08. Train/test behavioral cross-validation reveals neural correlates in mice
  • Nov 17 PM O10: PSTR223.05. Analyzing large-scale neural data with Suite2p
  • Nov 19 AM R8: PSTR394.02. Impact of eye movements and orofacial movements on mouse visual cortex
  • Nov 19 PM Q9: PSTR450.05. Spatial or temporal prediction in mouse visual cortex
  • Nov 19 PM S8: PSTR451.12. A critical initialization for biological neural networks
• Congrats to Qingqing Zhang et al, preprint now out on Spatial predictive coding in visual cortical neurons!
• Fengtong Du’s paper on minimodels of visual cortical neurons in mice and monkeys now published! News coverage
• Lin Zhong’s paper on unsupervised learning now published! News coverage
• Cellpose3 now published! News coverage
• 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

Resources

• About HHMI Janelia Research Campus
• HHMI’s values
• Being a postdoc at Janelia

Talks

• Cellpose3 talk+tutorial
• 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

• How Brains Learn & Compute: Neuroscience Meets AI with Dr. Marius Pachitariu, Mind & Matter Podcast

• New computational model could help shed light on how we see, Howard Hughes Medical Institute

• Doing This Might Actually Make You Smarter, Vice

• “Zoning Out” Actually Helps You Learn? Data From Up To 90,000 Brain Cells Says So, IFL Science

• Zoning out could be beneficial—and may actually help us learn faster, Howard Hughes Medical Institute

• Newest version of Cellpose can spot cell boundaries even in cloudy conditions, Howard Hughes Medical Institute

• 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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