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
- 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
- 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!
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
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
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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