BEP032: ephys -> microephys with {icephys, ecephys} modalities/suffix…

…es (#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

#1800 (comment)

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

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"]
 )
 }}
 

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

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.

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

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

src/schema/rules/files/raw/ephys.yaml → 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