Reflecting decision of having two separate datatypes under the Microe…

…lectrode Electrophysiology

#1800 (comment)

Consensus reached during working group meeting on 2024-05-15:

- modality = "Microelectrode Electrophysiology"
- datatypes = "icephys" and "ecephys"
- suffixes = "_icephys" and "_ecephys"

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"]
 )
 }}

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

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.

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

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