Marius Pachitariu [HTML] [SLIDES] [1, 2, 3] Primary: (PDF) Secondary: (PDF) (PDF)

The primary reading is Cunningham and Yu [1] and the two supplementary readings, Gao and Ganguli [2] and the Suite2p bioRxiv paper [3]. The primary reading offers a broad overview on dimensionality reduction in large scale recordings, and many examples of methods and ideas that have been used so far. Students could use these as inspiration to analyze the 10,000 cell data. Gao and Ganguli 2015 is a paper that starts building some mathematical intuition on the limitations of dimensionality reduction methods, and, finally, the Suite2p paper describes the full pipeline for going from raw data to inferred spike times.

References

[1]	J. P. Cunningham and B. M. Yu. Dimensionality reduction for large-scale neural recordings. Nature Neuroscience, 17(11):1500--1509, 2014.
[2]	Peiran Gao and Surya Ganguli. On simplicity and complexity in the brave new world of large-scale neuroscience. Current Opinion in Neurobiology, 32:148--155, 2015.
[3]	Marius Pachitariu, Carsen Stringer, Sylvia Schröder, Mario Dipoppa, L. Federico Rossi, Matteo Carandini, and Kenneth D. Harris. Suite2p: beyond 10,000 neurons with standard two-photon microscopy. bioRxiv, 2016.