Pachitariu + Stringer lab

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


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.




  • 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

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