[ENH] microelectrode electrophysiology specification (BEP032)

src/schema/objects/entities.yaml

@@ -331,12 +331,12 @@ split:
   display_name: Split
   description: |
     In the case of long data recordings that exceed a file size of 2Gb,
-    `.fif` files are conventionally split into multiple parts.
-    Each of these files has an internal pointer to the next file.
+    `.fif`, `.nwb`, `.nix` files are conventionally split into multiple parts.
+    Each of the `.fif` files has an internal pointer to the next file.
     This is important when renaming these split recordings to the BIDS convention.
 
     Instead of a simple renaming, files should be read in and saved under their
-    new names with dedicated tools like [MNE-Python](https://mne.tools/),
+    new names with dedicated tools like [MNE-Python](https://mne.tools/) for `.fif`,
     which will ensure that not only the filenames, but also the internal file pointers, will be updated.
 
     It is RECOMMENDED that `.fif` files with multiple parts use the `split-<index>` entity to indicate each part.

src/schema/objects/extensions.yaml

@@ -189,6 +189,11 @@ niigz:
   display_name: Compressed NIfTI
   description: |
     A compressed Neuroimaging Informatics Technology Initiative (NIfTI) data file.
+nix:
+  value: .nix
+  display_name: Neuroscience Information Exchange Format
+  description: |
+    A [Neuroscience Information Exchange](https://nixio.readthedocs.io) file.
 nwb:
   value: .nwb
   display_name: Neurodata Without Borders Format

src/schema/objects/modalities.yaml

@@ -35,3 +35,6 @@ motion:
 nirs:
   display_name: Near-Infrared Spectroscopy
   description: Data acquired with NIRS.
+ephys:
+  display_name: Electrophysiology
+  description: Data acquired using microelectrodes.

src/schema/objects/suffixes.yaml

@@ -571,6 +571,11 @@ electrodes:
   display_name: Electrodes
   description: |
     File that gives the location of (i)EEG electrodes.
+ephys:
+  value: ephys
+  display_name: Electrophysiology
+  description: |
+    Extra- or intracellular microelectrode recording data.
 epi:
   value: epi
   display_name: EPI
@@ -727,6 +732,11 @@ physio:
   display_name: Physiological recording
   description: |
     Physiological recordings such as cardiac and respiratory signals.
+probe:
+  value: probe
+  display_name: A recording probe
+  description: |
+    A probe with one or more recording contacts.
 probseg:
   value: probseg
   display_name: Probabilistic Segmentation

src/schema/rules/files/raw/channels.yaml

@@ -16,6 +16,16 @@ channels:
     acquisition: optional
     run: optional
 
+# ephys has one removed
+# TODO: see if to be added for consistency etc.
+channels__ephys:
+  $ref: rules.files.raw.channels.channels
+  datatypes:
+    - meg
+  entities:
+    $ref: rules.files.raw.channels.channels.entities
+    acquisition:
+
 # MEG has an additional entity available
 channels__meg:
   $ref: rules.files.raw.channels.channels

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

@@ -0,0 +1,18 @@
+---
+ephys:
+  suffixes:
+    - ephys
+  extensions:
+    - .nwb
+    # possible future: serialization in .zarr format to accompany .ome.zarr
+    # - .nwb.zarr
+    - .nix
+  datatypes:
+    - ephys
+  entities:
+    subject: required
+    session: optional
+    sample: optional
+    task: optional
+    run: optional
+    split: optional