We developed ndx-patterend-ogen, an NWB extension for holographic patterned optogenetic stimulation as part of the MouseV1 U19 project. We used this extension in a custom conversion pipeline, mousev1-to-nwb, converting data from their Nature Neuroscience 2024 paper, “The logic of recurrent circuits in the primary visual cortex.”

Working with Misha Ahrens’ lab at Janelia, we developed ahrens-lab-to-nwb, an open repo to convert data from their custom optical physiology acquisition system to NWB. This pipeline was used to standardize and publish the data associated with their Cell 2019 paper, “Glia Accumulate Evidence that Actions Are Futile and Suppress Unsuccessful Behavior.” The NWB dataset is published on DANDI as DANDI:000350/0.221219.1506. The dataset contains 5.9 TB of optical physiology data from zebrafish.

Working with Richard Axel’s lab at Columbia University, we developed axel-lab-to-nwb, a pipelin for converting their whole-brain fly two photon neurophysiology to NWB.

We developed dombeck-lab-to-nwb, an open NWB conversion pipeline including fiber photometry, ScanImage two-photon microscopy, suite2p, video camera, and DeepLabCut data as well as behavioral metrics.

We developed higley-lab-to-nwb, an open source NWB conversion pipeline including two-photon imaging data from ScanImage, custom ROI segmentation, wheel motion recorded with Spike2, and face motion captured with a CMOS camera.

We developed turner-lab-to-nwb, an open source NWB conversion pipeline using NeuroConv. The data was of extracellular electrophysiology using a TDT system on non-human primates (NHPs) during a 2-choice reaction time reaching task. The data also included spike sorting using Plexon software and trial events. This data was published as DANDI:000947/0.240510.2211, which contains 1 TB of neurophysiology data, which at the time of publication is the biggest NHP dataset. We also released this electronic notebook to demonstrate how to read and analyze the data directly from the archive. This data is associated with the article “Neural activity during a simple reaching task in macaques is counter to gating and rebound in basal ganglia–thalamic communication,” published in PLoS Biology, 2020.

We developed lerner-lab-to-nwb, an open source NWB conversion pipeline using NeuroConv.







We developed leifer_lab_to_nwb, an open source NWB conversion pipeline that uses NeuroConv. This dataset is calcium imaging from C. elegans from the Nature 2023 article, “Neural signal propagation atlas of Caenorhabditis elegans.”

We built buzsaki-lab-to-nwb, an open source NWB conversion pipeline that uses NeuroConv. This repository contains conversion code for several different conversions that have led to numerous datasets published on DANDI:

1. DANDI:000003/0.230629.1955, data from “Physiological Properties and Behavioral Correlates of Hippocampal Granule Cells and Mossy Cells,” Neuron, 2017
2. DANDI:000041/0.210812.1515, data from “Network Homeostasis and State Dynamics of Neocortical Sleep,” Neuron 2016
3. DANDI:000044/0.210812.1516, data from “Diversity in neural firing dynamics supports both rigid and learned hippocampal sequences,” Science, 2016
4. DANDI:000056/0.210812.1518, data from “Internally organized mechanisms of the head direction sense,” Nature Neuroscience, 2015
5. DANDI:000059/0.230907.2101, data from “Cooling of Medial Septum Reveals Theta Phase Lag Coordination of Hippocampal Cell Assemblies,” Neuron, 2020
6. DANDI:000061/0.210812.1517, data from “Reactivations of emotional memory in the hippocampus–amygdala system during sleep,” Nature Neuroscience, 2017
7. DANDI:000067/0.210812.1457, data from “Behavior-dependent short-term assembly dynamics in the medial prefrontal cortex,” Neuron 2008
8. DANDI:000114/0.230602.1643, data from “Oxytocin neurons enable social transmission of maternal behaviour,” Nature, 2021
9. DANDI:000166/0.220116.2037, data from “Layer-Specific Physiological Features and Interlaminar Interactions in the Primary Visual Cortex of the Mouse,” Neuron 2019
10. DANDI:000233/0.230223.0815, data from “A metabolic function of the hippocampal sharp wave-ripple,” Nature, 2021
11. DANDI:000552/0.230630.2304, data from “Preconfigured dynamics in the hippocampus are guided by embryonic birthdate and rate of neurogenesis,” Nature Neuroscience, 2022
12. DANDI:000568/0.230705.1633, data from “Probing subthreshold dynamics of hippocampal neurons by pulsed optogenetics,” Science, 2022

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