From b84fc96b1dc3c48cdb116731e5dd9d5ef3c9836a Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Thu, 25 Apr 2024 17:30:36 -0400 Subject: [PATCH 1/4] RF: to have cephys for modality/datatype and icephys and ecephys for suffixes --- .../microelectrode-electrophysiology.md | 12 ++++++------ src/schema/objects/datatypes.yaml | 9 +++++---- src/schema/objects/modalities.yaml | 6 +++--- src/schema/objects/suffixes.yaml | 17 +++++++++++------ src/schema/rules/files/raw/channels.yaml | 12 ++++++------ src/schema/rules/files/raw/ephys.yaml | 9 +++++---- 6 files changed, 36 insertions(+), 29 deletions(-) diff --git a/src/modality-specific-files/microelectrode-electrophysiology.md b/src/modality-specific-files/microelectrode-electrophysiology.md index 00b740de11..d49be47149 100644 --- a/src/modality-specific-files/microelectrode-electrophysiology.md +++ b/src/modality-specific-files/microelectrode-electrophysiology.md @@ -1,4 +1,4 @@ -# Microelectrode Electrophysiology +# Cellular 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/#ephys) +Several [example x datasets](https://bids-standard.github.io/bids-examples/#cephys) 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 `cephys` 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 `cephys` 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=["cephys"], + suffixes=["ecephys", "icephys", "events"] ) }} diff --git a/src/schema/objects/datatypes.yaml b/src/schema/objects/datatypes.yaml index b3751303b7..a70c17e8ab 100644 --- a/src/schema/objects/datatypes.yaml +++ b/src/schema/objects/datatypes.yaml @@ -11,6 +11,11 @@ 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 @@ -20,10 +25,6 @@ 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 diff --git a/src/schema/objects/modalities.yaml b/src/schema/objects/modalities.yaml index 701bd42b05..25a5f01edf 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: - display_name: Microelectrode Electrophysiology - description: Data acquired using microelectrodes. +cephys: + display_name: Cellular Electrophysiology + description: Electrophysiological data acquired at cellular level. diff --git a/src/schema/objects/suffixes.yaml b/src/schema/objects/suffixes.yaml index 53448792a8..e2dbe4879c 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 cephys 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..e473d1a1d4 100644 --- a/src/schema/rules/files/raw/channels.yaml +++ b/src/schema/rules/files/raw/channels.yaml @@ -16,11 +16,11 @@ channels: acquisition: optional run: optional -# ephys has an additional 'sample' entity -channels__ephys: +# cephys has an additional 'sample' entity +channels__cephys: $ref: rules.files.raw.channels.channels datatypes: - - ephys + - cephys entities: $ref: rules.files.raw.channels.channels.entities sample: optional @@ -66,11 +66,11 @@ coordsystem__eeg: $ref: rules.files.raw.channels.coordsystem.entities space: optional -# ephys has sample AND space entities -coordsystem__ephys: +# cephys has sample AND space entities +coordsystem__cephys: $ref: rules.files.raw.channels.coordsystem datatypes: - - ephys + - cephys 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/ephys.yaml index 460c99bed4..5621de9b52 100644 --- a/src/schema/rules/files/raw/ephys.yaml +++ b/src/schema/rules/files/raw/ephys.yaml @@ -1,14 +1,15 @@ --- -ephys: +cephys: suffixes: - - ephys + - ecephys + - icephys extensions: - .nwb # possible future: serialization in .zarr format to accompany .ome.zarr # - .nwb.zarr - .nix datatypes: - - ephys + - cephys entities: subject: required session: optional @@ -24,7 +25,7 @@ probes: extensions: - .tsv datatypes: - - ephys + - cephys entities: subject: required session: optional From 4c9b2de3aec08e9e17309f5e11558264fc4f6cfa Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Mon, 20 May 2024 16:07:37 -0400 Subject: [PATCH 2/4] 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 From d5649058b8e9c469f1d4717bce0a7562b7768780 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 31 May 2024 22:52:18 -0400 Subject: [PATCH 3/4] Adjust wording to Horea's recommendation --- src/schema/objects/datatypes.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/schema/objects/datatypes.yaml b/src/schema/objects/datatypes.yaml index 069824ea6a..112b6245fd 100644 --- a/src/schema/objects/datatypes.yaml +++ b/src/schema/objects/datatypes.yaml @@ -20,7 +20,7 @@ ecephys: value: ecephys display_name: Extracellular Electrophysiology description: | - Electrophysiological data acquired from an extracellular space + Electrophysiological data from an extracellular microelectrodes eeg: value: eeg display_name: Electroencephalography From 328ee7af2bc05e24096c95a3139470618edad90a Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Wed, 5 Jun 2024 13:25:17 -0400 Subject: [PATCH 4/4] Various fixups and tune ups to wording from code review --- .../microelectrode-electrophysiology.md | 4 ++-- src/schema/objects/datatypes.yaml | 4 ++-- src/schema/rules/files/raw/channels.yaml | 14 ++++++++------ 3 files changed, 12 insertions(+), 10 deletions(-) diff --git a/src/modality-specific-files/microelectrode-electrophysiology.md b/src/modality-specific-files/microelectrode-electrophysiology.md index dc36ad62d8..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/#microephys) +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 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 hardware 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: diff --git a/src/schema/objects/datatypes.yaml b/src/schema/objects/datatypes.yaml index 112b6245fd..1e57a7892d 100644 --- a/src/schema/objects/datatypes.yaml +++ b/src/schema/objects/datatypes.yaml @@ -20,7 +20,7 @@ ecephys: value: ecephys display_name: Extracellular Electrophysiology description: | - Electrophysiological data from an extracellular microelectrodes + Electrophysiological data from extracellular microelectrodes eeg: value: eeg display_name: Electroencephalography @@ -39,7 +39,7 @@ icephys: value: icephys display_name: Intracellular Electrophysiology description: | - Electrophysiological data acquired from an individual cell + Electrophysiological data acquired from intracellular or patch microelectrodes ieeg: value: ieeg display_name: Intracranial electroencephalography diff --git a/src/schema/rules/files/raw/channels.yaml b/src/schema/rules/files/raw/channels.yaml index e473d1a1d4..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 -# cephys has an additional 'sample' entity -channels__cephys: +# microephys has an additional 'sample' entity +channels__microephys: $ref: rules.files.raw.channels.channels datatypes: - - cephys + - 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 -# cephys has sample AND space entities -coordsystem__cephys: +# microephys has sample AND space entities +coordsystem__microephys: $ref: rules.files.raw.channels.coordsystem datatypes: - - cephys + - ecephys + - icephys entities: $ref: rules.files.raw.channels.coordsystem.entities sample: optional