Bep032 coord enum

src/appendices/coordinate-systems.md

@@ -248,6 +248,29 @@ Please note that `space-scanner` SHOULD NOT be used, it is mentioned in this spe
 | --------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | scanner               | The intrinsic coordinate system of the original image (the first entry of `RawSources`) after reconstruction and conversion to NIfTI or equivalent for the case of surfaces and dual volume/surface files. |
 
+## Microelectrode Electrophysiology Specific Coordinate Systems
+
+Restricted keywords for the `MicroephysCoordinateSystem` field in the
+`coordsystem.json` file for microelectrode electrophysiology datasets (both `icephys` and `ecephys`):
+
+| **Coordinate System** | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | **Reference**                                                                                                                  |
+| --------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------ |
+| Pixels                | If electrodes are localized in 2D space (only x and y are specified and z is `n/a`), then the positions in this file must correspond to the locations expressed in pixels on the photo/drawing/rendering of the electrodes on the brain. In this case, coordinates must be (row,column) pairs, with (0,0) corresponding to the upper left pixel and (N,0) corresponding to the lower left pixel.                                                                                        |                                                                                                                                |
+| Stereotaxic           | A generic stereotaxic coordinate system commonly used in animal neuroscience for surgical targeting and electrode localization. The origin is at bregma, a skull landmark defined as the intersection of the coronal and sagittal sutures. The x-axis corresponds to the anterior-posterior (AP) axis with posterior being positive. The y-axis corresponds to the dorsal-ventral (DV) or superior-inferior (SI) axis with ventral/inferior being positive. The z-axis corresponds to the medial-lateral (ML) axis with right being positive. Units are typically in millimeters or micrometers. |                                                                                                                                |
+| AllenCCFv3            | Allen Common Coordinate Framework version 3 ([RRID:SCR_020999](https://scicrunch.org/resolver/RRID:SCR_020999)), a 3D reference space for the mouse brain based on average anatomy. The framework provides a systematic way to map and compare data across different experiments and labs. Origin and orientation follow the Allen Institute conventions.                                                                                                                                                                                  | [doi:10.1016/j.cell.2020.04.007](https://doi.org/10.1016/j.cell.2020.04.007)                                                   |
+| WaxholmSpace          | A standardized 3D coordinate system for the rat brain ([RRID:SCR_001592](https://scicrunch.org/resolver/RRID:SCR_001592)) based on high-resolution imaging data. Part of the Waxholm Space atlas of the Sprague Dawley rat brain.                                                                                                                                                                                                                                                                                                          | [doi:10.1371/journal.pcbi.1001065](https://doi.org/10.1371/journal.pcbi.1001065)                                               |
+| WistarRatAtlas        | A multidimensional magnetic resonance histology atlas of the adult Wistar rat brain ([RRID:SCR_006288](https://scicrunch.org/resolver/RRID:SCR_006288)). This atlas provides high-resolution anatomical reference for rat brain studies.                                                                                                                                                                                                                                                                                                    | [doi:10.1016/j.neuroimage.2012.05.041](https://doi.org/10.1016/j.neuroimage.2012.05.041)                                       |
+| individual            | Subject-specific anatomical coordinate system derived from the individual subject's anatomy. The origin and orientation should be specified in `MicroephysCoordinateSystemDescription`. This coordinate system requires specifying an additional, subject-specific file to be fully defined.                                                                                                                                                                                             |                                                                                                                                |
+| Other                 | Use this for other coordinate systems and specify all required details in the `MicroephysCoordinateSystemDescription` field.                                                                                                                                                                                                                                                                                                                                                              |                                                                                                                                |
+
+If you believe a specific coordinate system should be added to the list
+of restricted keywords for microelectrode electrophysiology, please open a new issue on the
+[bids-standard/bids-specification GitHub repository](https://github.com/bids-standard/bids-specification/issues/new/choose).
+
+For detailed information about coordinate systems in microelectrode electrophysiology,
+including probe angles and anatomical reference points, see the
+[Microelectrode Electrophysiology specification](../modality-specific-files/microelectrode-electrophysiology.md#coordinate-system-json-_coordsystemjson).
+
 <!-- Link Definitions -->
 
 [common file level metadata fields]: ../derivatives/common-data-types.md#common-file-level-metadata-fields

src/modality-specific-files/microelectrode-electrophysiology.md

@@ -354,7 +354,7 @@ pipette02	patch-pipette	-1.8	-0.5	-2.2	30	0	0	R	Sutter	1	tip	Visual Cortex Layer
 pipette03	sharp-electrode	-3.2	1.2	-3.8	20	5	0	L	WPI	1	tip	Prefrontal Cortex Layer 5	PL5	Franklin-Paxinos
 ```
 
-For details on the surgical coordinate system used to describe probe placement during surgery (AP, ML, DV, angles, and 
+For details on the surgical coordinate system used to describe probe placement during surgery (AP, ML, DV, angles, and
 anatomical reference points), see the [Microelectrode Surgical Coordinates](../appendices/microelectrode-surgical-coordinates.md)
 appendix.
 

src/schema/meta/associations.yaml

@@ -108,7 +108,7 @@ probes:
   target:
     suffix: probes
     extension: .tsv
-    
+
 coordsystems:
   selectors:
     - datatype == 'emg'

src/schema/objects/enums.yaml

@@ -79,6 +79,16 @@ _iEEGCoordSys:
     - $ref: objects.enums.ACPC.value
     - $ref: objects.enums.ScanRAS.value
     - $ref: objects.enums.Other.value
+_MicroephysCoordSys:
+  type: string
+  enum:
+    - $ref: objects.enums.Pixels.value
+    - $ref: objects.enums.Stereotaxic.value
+    - $ref: objects.enums.AllenCCFv3.value
+    - $ref: objects.enums.WaxholmSpace.value
+    - $ref: objects.enums.WistarRatAtlas.value
+    - $ref: objects.enums.individual.value
+    - $ref: objects.enums.Other.value
 left_hemisphere:
   value: 'L'
   display_name: Left Hemisphere
@@ -1561,3 +1571,50 @@ microvascular:
   display_name: microvascular
   description: |
     The origin of a tissue: microvascular
+Stereotaxic:
+  value: Stereotaxic
+  display_name: Stereotaxic
+  description: |
+    A generic stereotaxic coordinate system commonly used in animal neuroscience for surgical
+    targeting and electrode localization. The origin is at bregma, a skull landmark defined as
+    the intersection of the coronal and sagittal sutures. The x-axis corresponds to the
+    anterior-posterior (AP) axis with posterior being positive. The y-axis corresponds to the
+    dorsal-ventral (DV) or superior-inferior (SI) axis with ventral/inferior being positive.
+    The z-axis corresponds to the medial-lateral (ML) axis with right being positive.
+    Units are typically in millimeters or micrometers. When using this coordinate system,
+    the specific anatomical reference point and units should be specified in
+    `MicroephysCoordinateSystemDescription`.
+AllenCCFv3:
+  value: AllenCCFv3
+  display_name: Allen CCF v3
+  description: |
+    Allen Common Coordinate Framework version 3 (RRID:SCR_020999), a 3D reference space for
+    the mouse brain based on average anatomy. The framework provides a systematic way to
+    map and compare data across different experiments and labs. Origin and orientation
+    follow the Allen Institute conventions.
+    Reference: Wang Q, Ding SL, Li Y, Royall J, Feng D, Lesnar P, Graddis N, Naeemi M, Facer B,
+    Ho A, Dolbeare T, Blanchard B, Dee N, Wakeman W, Hirokawa KE, Szafer A, Sunkin SM, Oh SW,
+    Bernard A, Phillips JW, Hawrylycz M, Koch C, Zeng H, Harris JA, Ng L. The Allen Mouse Brain
+    Common Coordinate Framework: A 3D Reference Atlas. Cell. 2020 May 14;181(4):936-953.e20.
+    [doi:10.1016/j.cell.2020.04.007](https://doi.org/10.1016/j.cell.2020.04.007).
+WaxholmSpace:
+  value: WaxholmSpace
+  display_name: Waxholm Space
+  description: |
+    A standardized 3D coordinate system for the rat brain (RRID:SCR_001592) based on
+    high-resolution imaging data. Part of the Waxholm Space atlas of the Sprague Dawley
+    rat brain. For more information, see
+    [https://www.nitrc.org/projects/whs-sd-atlas](https://www.nitrc.org/projects/whs-sd-atlas).
+    Reference: Hawrylycz M, Baldock RA, Burger A, Hashikawa T, Johnson GA, Martone M, Ng L,
+    Lau C, Larson SD, Nissanov J, Puelles L, Ruffins S, Verbeek F, Zaslavsky I, Boline J.
+    Digital atlasing and standardization in the mouse brain. PLoS Comput Biol. 2011 Feb 3;7(2):e1001065.
+    [doi:10.1371/journal.pcbi.1001065](https://doi.org/10.1371/journal.pcbi.1001065).
+WistarRatAtlas:
+  value: WistarRatAtlas
+  display_name: Wistar Rat Atlas
+  description: |
+    A multidimensional magnetic resonance histology atlas of the adult Wistar rat brain
+    (RRID:SCR_006288). This atlas provides high-resolution anatomical reference for rat brain studies.
+    Reference: Johnson GA, Calabrese E, Badea A, Paxinos G, Watson C. A multidimensional magnetic resonance
+    histology atlas of the Wistar rat brain. Neuroimage. 2012 Sep;62(3):1848-56.
+    [doi:10.1016/j.neuroimage.2012.05.041](https://doi.org/10.1016/j.neuroimage.2012.05.041).

src/schema/objects/files.yaml

@@ -138,5 +138,5 @@ probes:
   file_type: directory
   description: |
     A directory to store probe using the ProbeInterface specification format. This folder can be used to also store the associated probe figures.
-    This is primarily intended for use with Microelectrode Electrophysiology data, see more information in the 
+    This is primarily intended for use with Microelectrode Electrophysiology data, see more information in the
     [relevant section](SPEC_ROOT/modality-specific-files/microelectrode-electrophysiology.md#probeinterface-library).

src/schema/objects/metadata.yaml

@@ -2256,7 +2256,7 @@ MicroephysCoordinateSystem:
     on 2D coordinate systems.
     For a list of valid values for this field, see the associated glossary entry.
   anyOf:
-    # - $ref: objects.enums._MicroephysCoordSys
+    - $ref: objects.enums._MicroephysCoordSys
     - $ref: objects.enums._StandardTemplateCoordSys
 MicroephysCoordinateSystemDescription:
   name: MicroephysCoordinateSystemDescription

src/schema/rules/files/common/core.yaml

@@ -50,4 +50,4 @@ stimuli:
   path: stimuli
 probes:
   level: optional
-  path: probes
+  path: probes