Pachitariu + Stringer lab

Our lab is at HHMI Janelia Research Campus (near DC), in the Neuroscience and Computation departments.

We are recruiting postdocs, join us!

Research

The coordinated activity of large populations of neurons gives rise to perception, decision and action. The rules by which this activity is coordinated are not well understood. Our lab records from populations of ~50,000 neurons simultaneously at 3Hz, using two-photon calcium imaging with a large field of view mesoscope:

We use machine learning techniques to investigate the structure of the recorded activity, either in response to external stimuli such as virtual reality, or in response to the animal’s own actions. Learn more about our research here, see all publications here, and our code and data here.

News

• 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!
• Many lab members presented at SfN 2023, congrats to them for their great presentations!
• Carsen taught at the Deep Learning for Imaging course at Marine Biological Laboratory
• Check out the Rastermap preprint on biorxiv, code here

Resources

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

Talks

• 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

• Janelia scientists release state-of-the-art spike-sorting software Kilosort4

• 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

Powered by Quarto. © Marius Pachitariu & Carsen Stringer lab, 2023.