From 4c9b2de3aec08e9e17309f5e11558264fc4f6cfa Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Mon, 20 May 2024 16:07:37 -0400 Subject: [PATCH] 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" --- .../microelectrode-electrophysiology.md | 10 +++++----- src/schema/objects/datatypes.yaml | 15 ++++++++++----- src/schema/objects/modalities.yaml | 6 +++--- src/schema/objects/suffixes.yaml | 2 +- .../files/raw/{ephys.yaml => microephys.yaml} | 8 +++++--- 5 files changed, 24 insertions(+), 17 deletions(-) rename src/schema/rules/files/raw/{ephys.yaml => microephys.yaml} (89%) diff --git a/src/modality-specific-files/microelectrode-electrophysiology.md b/src/modality-specific-files/microelectrode-electrophysiology.md index d49be47149..dc36ad62d8 100644 --- a/src/modality-specific-files/microelectrode-electrophysiology.md +++ b/src/modality-specific-files/microelectrode-electrophysiology.md @@ -1,4 +1,4 @@ -# Cellular Electrophysiology +# Microelectrode Electrophysiology Support for Microelectrode Electrophysiology was developed as a [BIDS Extension Proposal](../extensions.md#bids-extension-proposals) [BEP032: Animal electrophysiology (ephys)](https://bids.neuroimaging.io/bep032). @@ -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/#cephys) +Several [example x 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 `cephys` 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 `cephys` systems. +The native file format is used in case conversion elicits the loss of crucial metadata specific to manufacturers and specific hardware systems. Metadata should be included alongside the data in the `.json` and `.tsv` files. The current list of allowed data file formats: @@ -50,7 +50,7 @@ and a guide for using macros can be found at --> {{ MACROS___make_filename_template( "raw", - datatypes=["cephys"], + datatypes=["ecephys", "icephys"], suffixes=["ecephys", "icephys", "events"] ) }} diff --git a/src/schema/objects/datatypes.yaml b/src/schema/objects/datatypes.yaml index a70c17e8ab..069824ea6a 100644 --- a/src/schema/objects/datatypes.yaml +++ b/src/schema/objects/datatypes.yaml @@ -11,16 +11,16 @@ beh: display_name: Behavioral Data description: | Behavioral data. -cephys: - value: cephys - display_name: Cellular Electrophysiology - description: | - Electrophysiological data acquired at cellular level. dwi: value: dwi display_name: Diffusion-Weighted Imaging description: | Diffusion-weighted imaging (DWI). +ecephys: + value: ecephys + display_name: Extracellular Electrophysiology + description: | + Electrophysiological data acquired from an extracellular space eeg: value: eeg display_name: Electroencephalography @@ -35,6 +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 an individual cell ieeg: value: ieeg display_name: Intracranial electroencephalography diff --git a/src/schema/objects/modalities.yaml b/src/schema/objects/modalities.yaml index 25a5f01edf..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. -cephys: - display_name: Cellular Electrophysiology - description: Electrophysiological data acquired at cellular level. +microephys: + display_name: Microelectrode Electrophysiology + description: Electrophysiological data acquired using microelectodes. diff --git a/src/schema/objects/suffixes.yaml b/src/schema/objects/suffixes.yaml index e2dbe4879c..f4f0c3f7af 100644 --- a/src/schema/objects/suffixes.yaml +++ b/src/schema/objects/suffixes.yaml @@ -763,7 +763,7 @@ probes: value: probes display_name: Implanted physical devices description: | - Physical devices used for recording cephys 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/ephys.yaml b/src/schema/rules/files/raw/microephys.yaml similarity index 89% rename from src/schema/rules/files/raw/ephys.yaml rename to src/schema/rules/files/raw/microephys.yaml index 5621de9b52..4a5aaaf5bc 100644 --- a/src/schema/rules/files/raw/ephys.yaml +++ b/src/schema/rules/files/raw/microephys.yaml @@ -1,5 +1,5 @@ --- -cephys: +microephys: suffixes: - ecephys - icephys @@ -9,7 +9,8 @@ cephys: # - .nwb.zarr - .nix datatypes: - - cephys + - ecephys + - icephys entities: subject: required session: optional @@ -25,7 +26,8 @@ probes: extensions: - .tsv datatypes: - - cephys + - ecephys + - icephys entities: subject: required session: optional