From a46e4391e627000342adf80288dab8c55340b441 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Wed, 5 Jun 2024 13:54:57 -0400 Subject: [PATCH] BEP032: ephys -> microephys with {icephys, ecephys} modalities/suffixes (#1806) * RF: to have "microephys" (Microelectrode physiology) for modality and icephys and ecephys for suffixes and datatypes * Reflecting decision of having two separate datatypes under the Microelectrode Electrophysiology https://github.com/bids-standard/bids-specification/issues/1800#issuecomment-2112715341 Consensus reached during working group meeting on 2024-05-15: - modality = "Microelectrode Electrophysiology" - datatypes = "icephys" and "ecephys" - suffixes = "_icephys" and "_ecephys" * Adjust wording to Horea's recommendation * Various fixups and tune ups to wording from code review --- .../microelectrode-electrophysiology.md | 10 +++++----- src/schema/objects/datatypes.yaml | 14 ++++++++++---- src/schema/objects/modalities.yaml | 4 ++-- src/schema/objects/suffixes.yaml | 17 +++++++++++------ src/schema/rules/files/raw/channels.yaml | 14 ++++++++------ .../files/raw/{ephys.yaml => microephys.yaml} | 11 +++++++---- 6 files changed, 43 insertions(+), 27 deletions(-) rename src/schema/rules/files/raw/{ephys.yaml => microephys.yaml} (85%) diff --git a/src/modality-specific-files/microelectrode-electrophysiology.md b/src/modality-specific-files/microelectrode-electrophysiology.md index 00b740de11..3c8fbb3377 100644 --- a/src/modality-specific-files/microelectrode-electrophysiology.md +++ b/src/modality-specific-files/microelectrode-electrophysiology.md @@ -16,14 +16,14 @@ You can also reach the moderators of this BEP through our [main discussion forum 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 x datasets](https://bids-standard.github.io/bids-examples/#ephys) +Several [example Microelectrode Electrophysiology datasets](https://bids-standard.github.io/bids-examples/#microephys) have been formatted using this specification and can be used for practical guidance when curating a new dataset. ## Primary data file formats -Unprocessed (animal) `ephys` data must be stored in an [open file format](https://en.wikipedia.org/wiki/Open_format), +Unprocessed microelectrode electrophysiology (`icephys` and `ecephys` modalities) data must be stored in an [open file format](https://en.wikipedia.org/wiki/Open_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 `ephys` systems. +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: @@ -50,8 +50,8 @@ and a guide for using macros can be found at --> {{ MACROS___make_filename_template( "raw", - datatypes=["ephys"], - suffixes=["ephys", "events"] + datatypes=["ecephys", "icephys"], + suffixes=["ecephys", "icephys", "events"] ) }} diff --git a/src/schema/objects/datatypes.yaml b/src/schema/objects/datatypes.yaml index b3751303b7..1e57a7892d 100644 --- a/src/schema/objects/datatypes.yaml +++ b/src/schema/objects/datatypes.yaml @@ -16,14 +16,15 @@ dwi: display_name: Diffusion-Weighted Imaging description: | Diffusion-weighted imaging (DWI). +ecephys: + value: ecephys + display_name: Extracellular Electrophysiology + description: | + Electrophysiological data from extracellular microelectrodes eeg: value: eeg display_name: Electroencephalography description: Electroencephalography -ephys: - value: ephys - display_name: Electrophysiology - description: Data acquired using microelectrodes. fmap: value: fmap display_name: Field maps @@ -34,6 +35,11 @@ func: display_name: Task-Based Magnetic Resonance Imaging description: | Task (including resting state) imaging data +icephys: + value: icephys + display_name: Intracellular Electrophysiology + description: | + Electrophysiological data acquired from intracellular or patch microelectrodes ieeg: value: ieeg display_name: Intracranial electroencephalography diff --git a/src/schema/objects/modalities.yaml b/src/schema/objects/modalities.yaml index 701bd42b05..73018dce44 100644 --- a/src/schema/objects/modalities.yaml +++ b/src/schema/objects/modalities.yaml @@ -35,6 +35,6 @@ motion: nirs: display_name: Near-Infrared Spectroscopy description: Data acquired with NIRS. -ephys: +microephys: display_name: Microelectrode Electrophysiology - description: Data acquired using microelectrodes. + description: Electrophysiological data acquired using microelectodes. diff --git a/src/schema/objects/suffixes.yaml b/src/schema/objects/suffixes.yaml index 53448792a8..f4f0c3f7af 100644 --- a/src/schema/objects/suffixes.yaml +++ b/src/schema/objects/suffixes.yaml @@ -573,6 +573,11 @@ dwi: display_name: Diffusion-weighted image description: | Diffusion-weighted imaging contrast (specialized T2 weighting). +ecephys: + value: ecephys + display_name: Extracellular Electrophysiology + description: | + Extracellular electrophysiological data. eeg: value: eeg display_name: Electroencephalography @@ -583,11 +588,6 @@ electrodes: display_name: Electrodes description: | File that gives the location of (i)EEG electrodes. -ephys: - value: ephys - display_name: Microelectrode Electrophysiology - description: | - Extra- or intracellular microelectrode recording data. epi: value: epi display_name: EPI @@ -617,6 +617,11 @@ hipCT: display_name: HiP-CT description: | Hierarchical Phase-Contrast Tomography imaging data +icephys: + value: icephys + display_name: Inracellular Electrophysiology + description: | + Intracellular electrophysiological data. ieeg: value: ieeg display_name: Intracranial Electroencephalography @@ -758,7 +763,7 @@ probes: value: probes display_name: Implanted physical devices description: | - Physical devices used for recording ephys data, whether chronically or acutely implanted. + Physical devices used for recording microelectrode electrophysiology data, whether chronically or acutely implanted. probseg: value: probseg display_name: Probabilistic Segmentation diff --git a/src/schema/rules/files/raw/channels.yaml b/src/schema/rules/files/raw/channels.yaml index e96c440bcf..ea1b164483 100644 --- a/src/schema/rules/files/raw/channels.yaml +++ b/src/schema/rules/files/raw/channels.yaml @@ -16,11 +16,12 @@ channels: acquisition: optional run: optional -# ephys has an additional 'sample' entity -channels__ephys: +# microephys has an additional 'sample' entity +channels__microephys: $ref: rules.files.raw.channels.channels datatypes: - - ephys + - icephys + - ecephys entities: $ref: rules.files.raw.channels.channels.entities sample: optional @@ -66,11 +67,12 @@ coordsystem__eeg: $ref: rules.files.raw.channels.coordsystem.entities space: optional -# ephys has sample AND space entities -coordsystem__ephys: +# microephys has sample AND space entities +coordsystem__microephys: $ref: rules.files.raw.channels.coordsystem datatypes: - - ephys + - ecephys + - icephys entities: $ref: rules.files.raw.channels.coordsystem.entities sample: optional diff --git a/src/schema/rules/files/raw/ephys.yaml b/src/schema/rules/files/raw/microephys.yaml similarity index 85% rename from src/schema/rules/files/raw/ephys.yaml rename to src/schema/rules/files/raw/microephys.yaml index 460c99bed4..4a5aaaf5bc 100644 --- a/src/schema/rules/files/raw/ephys.yaml +++ b/src/schema/rules/files/raw/microephys.yaml @@ -1,14 +1,16 @@ --- -ephys: +microephys: suffixes: - - ephys + - ecephys + - icephys extensions: - .nwb # possible future: serialization in .zarr format to accompany .ome.zarr # - .nwb.zarr - .nix datatypes: - - ephys + - ecephys + - icephys entities: subject: required session: optional @@ -24,7 +26,8 @@ probes: extensions: - .tsv datatypes: - - ephys + - ecephys + - icephys entities: subject: required session: optional