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Microelectrode Electrophysiology

Support for Microelectrode Electrophysiology was developed as a BIDS Extension Proposal BEP032: Animal electrophysiology (ephys).

Please see Citing BIDS on how to appropriately credit this extension when referring to it in the context of the academic literature.

This BEP has been initiated by members of the INCF Working Group on Standardized Data Structures, that was initiated in 2020 to develop a set of specifications and tools that would allow the standardization of a directory structure for experimental data recorded with animal models in neuroscience, and its associated metadata.

Please consider joining this working group if you would like to contribute to this effort. You can also reach the moderators of this BEP through our main discussion forum, where you can participate in existing discussions or raise new questions / issues.

Most core principles of the original BIDS and particulars of BIDS-iEEG specification are adopted for this modality as well, though some special considerations and additional fields were added.

Several example Microelectrode Electrophysiology datasets have been formatted using this specification and can be used for practical guidance when curating a new dataset.

Primary data file formats

Unprocessed microelectrode electrophysiology (microephys) modality data (of icephys or ecephys datatypes) must be stored in an open file format, while the native format, if different, can be stored in an optional sourcedata/ directory. The native file format is used in case conversion elicits the loss of crucial metadata specific to manufacturers and specific acquisition systems. Metadata should be included alongside the data in the .json and .tsv files. The current list of allowed data file formats:

Format Extension(s) Description
Neuroscience Information Exchange Format .nix A generic and open framework with an hdf5 backend and a defined interface to many ephys formats via the Neo library. The .nix file has to contain a valid Neo structure.
Neurodata Without Borders .nwb BRAIN Initiative Data Standard based on an hdf5 backend ...

Both of these formats can also store essential metadata of the datasets. Some of these need to be duplicated in BIDS .tsv and .json sidecar files. Even though the duplication requires additional effort to ensure the consistency of the data, it provides a number of advantages: - Making the dataset easier for humans to scan as essential information is easily accessible without loading the data files - The dataset follows the BIDS standard and can benefit from tools building on top of this standard, starting with bids-validator. - It simplifies the separation of data and basic metadata, for example to publish a dataset in a light-weight fashion with access to the data files on request (as implemented by DataLad).

Template:

sub-<label>/
    [ses-<label>/]
        ecephys/
            sub-<label>[_ses-<label>][_sample-<label>][_task-<label>][_acq-<label>][_run-<index>][_split-<index>]_ecephys.nix
            sub-<label>[_ses-<label>][_sample-<label>][_task-<label>][_acq-<label>][_run-<index>][_split-<index>]_ecephys.nwb
            sub-<label>[_ses-<label>][_sample-<label>][_task-<label>][_acq-<label>][_run-<index>][_split-<index>]_icephys.nix
            sub-<label>[_ses-<label>][_sample-<label>][_task-<label>][_acq-<label>][_run-<index>][_split-<index>]_icephys.nwb
        icephys/
            sub-<label>[_ses-<label>][_sample-<label>][_task-<label>][_acq-<label>][_run-<index>][_split-<index>]_ecephys.nix
            sub-<label>[_ses-<label>][_sample-<label>][_task-<label>][_acq-<label>][_run-<index>][_split-<index>]_ecephys.nwb
            sub-<label>[_ses-<label>][_sample-<label>][_task-<label>][_acq-<label>][_run-<index>][_split-<index>]_icephys.nix
            sub-<label>[_ses-<label>][_sample-<label>][_task-<label>][_acq-<label>][_run-<index>][_split-<index>]_icephys.nwb
Legend:

  • For more information about filename elements (for example, entities, suffixes, extensions), follow the links embedded in the filename template.

  • Filename entities or directories between square brackets (for example, [_ses-<label>]) are OPTIONAL.

  • Some entities may only allow specific values, in which case those values are listed in <>, separated by |.

  • _<suffix> means that there are several (>6) valid suffixes for this filename pattern.

  • .<extension> means that there are several (>6) valid extensions for this file type.

  • [.gz] means that both the unzipped and gzipped versions of the extension are valid.