Collaborative manuscript for extending BIDS to microelectrode electrophysiology.
Standards-compliance is a crucial aspect of open science, as it facilitates both collaboration and transparency. The Brain Imaging Data Structure (BIDS) is an increasingly widely used set of specifications, and is being actively expanded beyond its initial scope of brain imaging. Animal research methods have received increasing attention in BIDS, and among these, electrophysiological methods have been of considerable interest. Here we present the extension of BIDS to “microelectrode electrophysiology”, a term coined to denote electrophysiological recordings with microelectrodes, including intracellular, extracellular, and tissue-level electrophysiology. This BIDS extension proposal, BEP 032, deals with the challenges arising from the diverse range of technologies in electrophysiology and converges on signal and electrode channels as common metadata denominators, with the open standards NIX and NWB as allowed data formats. It provides a homogeneous standard for various microelectrode techniques, including patch clamp and multielectrode array recordings. Moreover, it tackles integration with behavioural data and electrode localization specifications. The directory layout is consistent with BIDS, allowing intuitive data structure recognition at-a-glance even for non-experts. Our work provides not only access to cutting-edge standards for researchers in electrophysiology, but also a crucial extension to BIDS, providing a handling template for metadata aspects with relevance beyond electrophysiology.
- Writing suggestions: https://bids.neuroimaging.io/extensions/process.html#bep-paper-writing-suggestion
- GitHub issue #1800: bids-standard/bids-specification#1800
- Discussion document: https://docs.google.com/document/d/1GlHr3Go5sR2o_zmxyCU6Sq1W1LLAaV_XZcKpeG_iBFw/edit?tab=t.0
- OpenMinds extracellular electrophysiology: https://openminds-documentation.readthedocs.io/en/latest/instance_libraries/terminologies/technique.html#extracellularelectrophysiology
- OBI ontology: https://ontobee.org/ontology/OBI?iri=http://purl.obolibrary.org/obo/OBI_0000454
- InterLex: https://scicrunch.org/scicrunch/interlex/view/ilx_0739521
- AIND schema (surgery info compatibility): https://aind-data-schema.readthedocs.io/en/stable/acquisition.html
There have been significant developments in neuroimaging and electrophysiology techniques used in neuroscience over the last few years. Imaging techniques such as MRI, fMRI, or PET provide detailed brain activity maps across space. On the other hand, understanding neuronal dynamics requires high-resolution electrophysiological methods, including extracellular and intracellular recording.
Efforts are being made to standardize these heterogeneous datasets generated by micro-electrode electrophysiology techniques, making both a need for this and the benefits more visible. These methods involve using language-agnostic common object data models (see Neo), and comprehensive data formats (see NWB, NIX, ABF, NDF, OpenEphys etc.) [add more]. While these strategies call attention to the significance of standardization, they also suggest that there is fragmentation within current efforts, which needs to be addressed through a unified and intuitive approach that encourages widespread adoption.
In this context, we propose an extension of the Brain Imaging Data Structure (BIDS) – a standard that has already gained wide acceptance – to incorporate "microelectrode electrophysiology, " including intracellular, extracellular, and tissue-level electrophysiology.
- Modality: The category of brain data recorded by a file. For MRI data, different pulse sequences are considered distinct modalities, such as T1w, bold or dwi. For passive recording techniques, such as EEG, MEG or iEEG, the technique is sufficiently uniform to define the modalities eeg, meg and ieeg. When applicable, the modality is indicated in the suffix. The modality may overlap with, but should not be confused with the data type.
- Data type: A functional group of different types of data. Data files are contained in a directory named for the data type. In raw datasets, the data type directory is nested inside subject and (optionally) session directories.
- Suffix: An alphanumeric string that is part of a filename, located after all entities and following a final
_, right before the file extension. For example, it iseeginsub-05_task-matchingpennies_eeg.vhdr.
The modality described in this extension and that characterizes the introduced datasets is termed 'Microelectrode Electrophysiology'. This choice balances specificity, clarity and alignment with the current BIDS standard and common community usage.
Specificity and Distinction from Existing Modalities Microelectrode electrophysiology establishes a clear distinction from other electrophysiological recording techniques already described by BIDS, such as EEG and iEEG, with the term 'micro' referring to the typical spatial scale of electrode contacts. Hence, the modality name differentiates these recordings from broader electrophysiological categories while maintaining clarity and agreement with the conventional community usage.
Maintaining Modularity and Extensibility of BIDS The proposed choice is a foresighted approach for maintaining the modularity and extensibility of BIDS. As new electrophysiological techniques are introduced in the future, a specific and descriptive naming convention would help prevent probable namespace conflicts, ensuring new modalities and data types can integrate seamlessly without breaking the current standard.
Separation of Data types and Suffixes As for the datatype, we introduce "icephys" for intracellular electrophysiology and "ecephys" for extracellular electrophysiology. BIDS datatypes categorize functional groups of data and metadata files and subsequently serve as the directory name.
- TODO: Do we add more arguments for some of the rejected options like 'Cellular'?
- Refer discussions from: bids-standard/bids-specification#1800
- Ontologies and terminologies:
- Also see discussion document: https://docs.google.com/document/d/1GlHr3Go5sR2o_zmxyCU6Sq1W1LLAaV_XZcKpeG_iBFw/edit?tab=t.0
- Note from 20250820 Meeting: Review compatibility with AIND (https://aind-data-schema.readthedocs.io/en/stable/acquisition.html) schema
The following sections are currently defined in the manuscript structure:
- Modality and Data Type Nomenclature
- BIDS Terminology
- Specificity and Distinction from Existing Modalities
- Maintaining Modularity and Extensibility of BIDS
- Separation of Data types and Suffixes
- Related BIDS Modalities
- Data Types: icephys and ecephys
- Surgery Information
- Age and Birthdate
- Electrode Locations
- Coordinate system
- Electrode Placement Image
- Channel type enum additions
- scans.tsv
- events.tsv
- NWB
- NIX
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