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Conversion of multimodal data between Losonczy Lab and NWB:N formats

Key Investigators

Sebi Rolotti (Losonczy Lab, Columbia University)

Project Description

Our lab collects 2-photon imaging and extracellular electrophysiological data in awake behaving mice. Our overall goal is to increase the interoperability of our data structures and formats with those of NWB. We already have fairly well developed repositories for working with our data, including a public package for sequential imaging data (SIMA) as well as in-house lab analysis bundle (LAB) for associating and analyzing these various data formats. We therefore hope to allow for seamless import from and export to NWB using the APIs for these repos.

Objectives

  1. Objective A. Determine how to best store (multi-plane) imaging data in NWB, potentially including pre-processing information such as motion correction displacements and ROIs.
  2. Objective B. Determine how to store extracted calcium signals, multi-channel electrophysiological signals, behavior data alongside imaging.
  3. Objective C. Add import and export functions for imaging data to SIMA API
  4. Objective D. Add import and export functions for all data types to LAB API

Approach and Plan

Progress and Next Steps

Materials

Background and References

Source code for SIMA: https://github.com/losonczylab/sima

SIMA API Documentation: http://www.losonczylab.org/sima/1.3.2/

SIMA Publication: https://www.frontiersin.org/articles/10.3389/fninf.2014.00080/full

MWE Source code for LAB: https://github.com/losonczylab/Zaremba_NatNeurosci_2017/tree/master/losonczy_analysis_bundle/lab