This Jupyter notebook was created from a BootCamp class hosted by the Ahrens Lab in HHMI Janelia (tutors Takashi Kawashima and Mika Rubinov). The goal of this class is to learn the basics of data analysis for large-scale calcium imaging experiments. In our experiment, calcium activities of ~100,000 neurons were simuntaneously recorded from brains of larval zebrafish, behaving in a virtual reality environment [ref 1-3].
[1] Whole-brain functional imaging at cellular resolution using light-sheet microscopy. Ahrens MB, Orger MB, Robson DN, Li JM, Keller PJ; Nature Methods. 2013 May;10(5):413-20. doi: 10.1038/nmeth.2434
[2] Mapping brain activity at scale with cluster computing. Freeman J, Vladimirov N, Kawashima T, Mu Y, Sofroniew NJ, Bennett DV, Rosen J, Yang C, Looger LL, Ahrens MB Nature Methods. 2014 Jul 27;11(9):941-950. doi: 10.1038/nmeth.3041
[3] Light-sheet functional imaging in fictively behaving zebrafish. Vladimirov N, Mu Y, Kawashima T, Bennett DV, Yang C, Looger LL, Keller PJ, Freeman J, Ahrens MB Nature Methods. 2014 Jul 27;11(9):883-4. doi: 10.1038/nmeth.3040