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We created the NWB pipeline based on Patient Data Manager (PDM) and MultiExpAnalaysis by Emily and Chris Dao, which are based on wave_clus by Quian Quiroga, R. [1] It reads raw data from Neuralynx and Blackrock and saves the processed results in both .mat and .nwb format. This document lists the requirements of this pipeline based on the discussion with John, Soraya, and Emily. For now, we focus on MovieParadigm (a sequence of experiments watching 24 series) and Screening (a pilot experiment screening concept neurons).

MovieParadigm is composed of multiple experiments, which create challenges in the consistency of spike sorting and make manual spike clustering cumbersome. We combine the results of automatic spike sorting to address this issue.

For multi-exp analysis, we save the CSC separately, as this will let others be aware of the gaps between experiments. Spikes will still be combined, as we need all spikes for clustering. All the timestamps will be saved in seconds. Each experiment/combined experiment will have a timestampsStart, the start timestamp of the experiment/first experiment in multi-experiment analysis. The Unix timestamp can be recovered by adding it to the spike timestamps.

References

[1] F. J. Chaure, H. G. Rey and R. Quian Quiroga. A novel and fully automatic spike sorting implementation with variable number of features. Journal of Neurophysiology; 2018. https://doi.org/10.1152/jn.00339.2018