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Convert to NWB

Compute Credits

This tool uses 1.0 compute credits per hour.

Overview

This tool can be used to convert miniscope movies, cell sets, neural events, and behavior videos including nVision movies to the Neurodata Without Borders (NWB) format.

Input Data

Input Data Description Required
Miniscope Movie Miniscope movie to include in the NWB file (.isxd) No
Cell Set Cell set to include in the NWB file No
Neural Events Neural events to include in the NWB file No
Behavior Video Behavior video to include in the NWB file (.mp4, .avi, .isxb) No

Requirements

  • At least 1 input data file must be chosen.
  • The input files must come from a single recording session.
  • Neural events must be accompanied by a corresponding cell set.

Parameters

Parameter Description Required
Session Description Description of the session where the data was generated No
Subject Identifier Unique identifier for the subject No
Subject Species The species of the subject. The formal Latin binomial nomenclature (e.g. Mus musculus for a mouse) should be used for compatibility with DANDI. No
Subject Age The age of the subject. The ISO 8601 duration format (e.g. P90D for 90 days old) should be used for compatibility with DANDI. No
Subject Sex The sex of the subject. One of the following values should be used for compatibility with DANDI: M for male, F for female, U for unknown, O for other. No

Requirements for Compatibility with DANDI

Export to DANDI is compatible with Neurodata Without Borders files (.nwb) that meet the requirements outlined below. DANDI's terms and policies can also be consulted for additional details.

  • Session Metadata
    • A session description must be specified.
  • Subject Metadata
    • The subject identifier must be specified.
    • The subject species must be specified using formal latin binomial nomenclature (e.g. Mus musculus for a mouse).
    • The subject age must be specified using the ISO 8601 format (e.g. P90D for 90 days old).
    • The subject sex must be set to one of the following values: M for male, F for female, U for unknown, and O for other.
  • Behavior Video
    • The behavior video must use one of the following file extensions: mp4, avi, wmv, mov, flv, mkv.
    • If you wish to include a nVision movie (.isxb), it must first be converted to one of the supported file extensions. This can be achieved using the Convert Inscopix Movie to MP4 tool.

Description

Following the NWB standards, recording metadata is extracted from the input files and used to construct the relevant entities within the NWB file. A device entity is created for the miniscope to store details about the acquisition setup. Imaging data from the miniscope is stored in a OnePhotonSeries. The cell set is stored as a RoiResponseSeries, which pair neural traces with the corresponding regions of interest in the imaging plane. Neural events are associated with individual cells by storing the timestamp and amplitude of each event as data columns attached to the PlaneSegmentation. If a behavior video is selected, a behavior camera device is created along with an ImageSeries referencing the external video file. The output nwb file is named using the following convention: sub-{subject_id}_ses-{session_id}.nwb, where subject_id is the Subject Identifier value supplied in the analyis table and session_id is the start date of the recording (YYYYMMDD). If no subject identifier is specified, the file name is simplified to ses-{session_id}.nwb. If a behavior video is supplied, a zip file containing the nwb file and behavior video is produced and named using the same convention.

Output Data

NWB Data

When no behavior video is selected, the output consists of a single nwb file containing the data selected for conversion. When a behavior video is selected, the output consists of a single zip file containing one nwb file and the behavior video.

Next Steps

The output of this tool can be transferred to the DANDI archive using the Export to DANDI feature.