Catalogue of NeuroConv Projects#
This is a catalogue of real-world examples of labs using NeuroConv to convert their data to NWB files. Each project listed contains a description and a link to an open GitHub repository. Many of these projects use advanced customization features beyond what is demonstrated in the conversion gallery.
Note
Many of these projects have pinned a specific minor version of NeuroConv, or its predecessor, nwb-conversion-tools (NCT). We have organized each pipeline according to the version used in descending order (newest version first).
NeuroConv v0.3#
froemke-lab-to-nwb#
Dr. Robert Froemke’s Lab at NYU converted electrophysiology, photometry, and behavior to create dandisets:
000114 associated with the Carcea et al. Nature 2021 paper, “Oxytocin neurons enable social transmission of maternal behaviour”
000249 associated with the Schiavo et al. Nature 2020 paper, “Innate and plastic mechanisms for maternal behaviour in auditory cortex”.
NeuroConv v0.2#
ahrens-lab-to-nwb#
Dr. Misha Ahrens’ lab at Janelia converted the imaging data corresponding to the publication Mu Y, Bennett DV, Rubinov M, Narayan S, Yang CT, Tanimoto M, Mensh BD, Looger LL, Ahrens MB. Glia Accumulate Evidence that Actions Are Futile and Suppress Unsuccessful Behavior. Cell. 2019 and shared the data on the DANDI archive. In this experiment, paralyzed zebra-fish were placed in a virtual reality environment which systematically responded to their attempts to swim by either mimicking movement effects within the environment or not (test of futility). While the subject attempts to engage in swimming behaviors, a light-sheet microscope performs whole-brain scans tracking florescence activity of neurons, glia, or both depending on the session.
murthy-lab-to-nwb#
This project from Dr. Mala Murthy’s lab at Princeton is focused on converting data from an upcoming paper related to mating behaviors. This pipeline features multiple subjects, pose estimation through SLEAP, and visual stimulus reconstruction (from the fly’s perspective).
fee-lab-to-nwb#
Dr. Michale Fee’s lab at MIT is using this pipeline to convert and share data related to several upcoming publications utilizing both optical imaging and extracellular electrophysiology. These pipelines include encoding and visualization of complex hierarchical audio signals which are compared directly to temporally aligned neural activity.
NCT v0.9#
buzsaki-lab-to-nwb#
These pipelines were built for Dr. Gyorgy Buzsáki’s lab at NYU as part of the Ripple U19 project. The pipelines provided here have converted and published data from 7 major publications with over 14 TB of data combined on the DANDI Archive. Most of the data consists of raw recordings, LFP, spike sorted units, and behavior with can consist of a mix of mental state tracking, position tracking through mazes, and trial stimulus events.
shenoy-lab-to-nwb#
These pipelines were built for Dr. Krishna Shenoy’s lab at Stanford and illustrate conversion of extracellular recordings from Utah arrays and Neuropixels in primates.
brody-lab-to-nwb#
This project with Dr. Carlos Brody’s lab at Princeton served two purposes: to allow the conversion of older data from Neuralynx and SpikeGadgets to NWB, and also their newer, larger data using Neuropixels (SpikeGLX). These recordings, some of which exceeded more than 250 GB (several hours worth!), were paired with rich trials tables containing categorical events and temporal stimuli.
NCT v0.8#
feldman-lab-to-nwb#
Dr. Dan Feldman’s lab at UC Berkeley utilizes a Neuropixels (SpikeGLX) system along with multiple sophisticated behavior systems for manipulating whisker stimulation in mice. These give rise to very complex trials tables tracking multiple event times throughout the experiments, including multiple event trains within trials.
NCT v0.7.0#
tank-lab-to-nwb#
In this project, we worked with Dr. David Tank’s lab at Princeton to package data from Neuropixel (SpikeGLX) recordings of subjects navigating a virtual reality. Behavior contains a variety of NWB data types including positional and view angle over time, collision detection, and more. This data utilizes a custom extension for parsing experiment metadata.
mease-lab-to-nwb#
In this project, we worked with the Groh Lab. Utilizing the CED recording interface, this project paired ecephys channels with optogenetic stimulation via laser pulses, and mechanical pressure stimulation over time - all of which are channels of data extracted from the common .smrx files!
giocomo-lab-to-nwb#
This project from Dr. Lisa Giocomo’s lab at Stanford features conversion pipelines that handle raw and processed data from SpikeGLX and from calcium imaging.