feat(microephys): add brain atlas coordinate systems for rodents and primates

Add new MicroephysCoordinateSystem options for commonly used stereotaxic
atlases:
- PaxinosWatson: rat brain atlas
- FranklinPaxinos: mouse brain atlas
- SwansonRat: rat brain atlas
- CHARM: macaque cortical hierarchy atlas
- D99: Saleem-Logothetis macaque atlas
- PaxinosMacaque: macaque stereotaxic atlas
- MarmosetBrainAtlas: marmoset brain atlas

These additions expand support for microelectrophysiology recordings
across multiple species with widely-used reference coordinate systems.

Author: bendichter

src/appendices/coordinate-systems.md

@@ -314,6 +314,71 @@ Restricted keywords for the `MicroephysCoordinateSystem` field in the
       </td>
       <td><a href="https://doi.org/10.1016/j.neuroimage.2012.05.041">doi:10.1016/j.neuroimage.2012.05.041</a></td>
     </tr>
+    <tr>
+      <td>PaxinosWatson</td>
+      <td>
+        The Paxinos and Watson rat brain atlas (<a href="https://scicrunch.org/resolver/RRID:SCR_006369">RRID:SCR_006369</a>),
+        a widely used stereotaxic coordinate system for the rat brain.
+        Provides standardized coordinates based on skull landmarks (bregma, lambda) for targeting brain structures.
+        Multiple editions available; users should specify the edition used in <code>MicroephysCoordinateSystemDescription</code>.
+      </td>
+      <td>Paxinos G, Watson C. The Rat Brain in Stereotaxic Coordinates. Academic Press.</td>
+    </tr>
+    <tr>
+      <td>FranklinPaxinos</td>
+      <td>
+        The Franklin and Paxinos mouse brain atlas (<a href="https://scicrunch.org/resolver/RRID:SCR_007127">RRID:SCR_007127</a>),
+        a widely used stereotaxic coordinate system for the mouse brain.
+        Provides standardized coordinates based on skull landmarks (bregma, lambda) for targeting brain structures.
+        Multiple editions available; users should specify the edition used in <code>MicroephysCoordinateSystemDescription</code>.
+      </td>
+      <td>Franklin KBJ, Paxinos G. The Mouse Brain in Stereotaxic Coordinates. Academic Press.</td>
+    </tr>
+    <tr>
+      <td>SwansonRat</td>
+      <td>
+        The Swanson rat brain atlas (<a href="https://scicrunch.org/resolver/RRID:SCR_007367">RRID:SCR_007367</a>),
+        a widely used stereotaxic coordinate system for the rat brain.
+        Provides detailed cytoarchitectonic parcellation and standardized coordinates for targeting brain structures.
+        Multiple editions available; users should specify the edition used in <code>MicroephysCoordinateSystemDescription</code>.
+      </td>
+      <td>Swanson LW. Brain Maps: Structure of the Rat Brain. Elsevier.</td>
+    </tr>
+    <tr>
+      <td>CHARM</td>
+      <td>
+        Cortical Hierarchy Atlas of the Rhesus Macaque (<a href="https://scicrunch.org/resolver/RRID:SCR_023283">RRID:SCR_023283</a>),
+        a modern MRI-based atlas for the macaque brain.
+        Provides hierarchical cortical parcellation based on anatomical connectivity patterns.
+      </td>
+      <td><a href="https://doi.org/10.1016/j.neuroimage.2021.117997">doi:10.1016/j.neuroimage.2021.117997</a></td>
+    </tr>
+    <tr>
+      <td>D99</td>
+      <td>
+        Digital version of the Saleem and Logothetis macaque brain atlas (<a href="https://scicrunch.org/resolver/RRID:SCR_014606">RRID:SCR_014606</a>).
+        Provides detailed parcellation of the rhesus macaque brain based on histological sections.
+      </td>
+      <td><a href="https://doi.org/10.1093/cercor/bhw248">doi:10.1093/cercor/bhw248</a></td>
+    </tr>
+    <tr>
+      <td>PaxinosMacaque</td>
+      <td>
+        The Paxinos rhesus macaque brain atlas (<a href="https://scicrunch.org/resolver/RRID:SCR_016249">RRID:SCR_016249</a>),
+        a stereotaxic coordinate system for the macaque brain.
+        Provides standardized coordinates based on stereotaxic landmarks for targeting brain structures.
+        Multiple editions available; users should specify the edition used in <code>MicroephysCoordinateSystemDescription</code>.
+      </td>
+      <td>Paxinos G, Huang XF, Petrides M, Toga AW. The Rhesus Monkey Brain in Stereotaxic Coordinates. Academic Press.</td>
+    </tr>
+    <tr>
+      <td>MarmosetBrainAtlas</td>
+      <td>
+        A standardized 3D coordinate system for the common marmoset brain (<a href="https://scicrunch.org/resolver/RRID:SCR_023286">RRID:SCR_023286</a>).
+        Provides high-resolution anatomical reference for marmoset brain studies.
+      </td>
+      <td><a href="https://doi.org/10.1016/j.neuroimage.2017.12.004">doi:10.1016/j.neuroimage.2017.12.004</a></td>
+    </tr>
     <tr>
       <td>individual</td>
       <td>

src/schema/objects/enums.yaml

@@ -87,6 +87,13 @@ _MicroephysCoordSys:
     - $ref: objects.enums.AllenCCFv3.value
     - $ref: objects.enums.WaxholmSpace.value
     - $ref: objects.enums.WistarRatAtlas.value
+    - $ref: objects.enums.PaxinosWatson.value
+    - $ref: objects.enums.FranklinPaxinos.value
+    - $ref: objects.enums.SwansonRat.value
+    - $ref: objects.enums.CHARM.value
+    - $ref: objects.enums.D99.value
+    - $ref: objects.enums.PaxinosMacaque.value
+    - $ref: objects.enums.MarmosetBrainAtlas.value
     - $ref: objects.enums.individual.value
     - $ref: objects.enums.Other.value
 left_hemisphere:
@@ -1618,3 +1625,62 @@ WistarRatAtlas:
     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).
+PaxinosWatson:
+  value: PaxinosWatson
+  display_name: Paxinos-Watson
+  description: |
+    The Paxinos and Watson rat brain atlas (RRID:SCR_006369), a widely used stereotaxic coordinate system for the rat brain.
+    Provides standardized coordinates based on skull landmarks (bregma, lambda) for targeting brain structures.
+    Reference: Paxinos G, Watson C. The Rat Brain in Stereotaxic Coordinates. Academic Press.
+    Multiple editions available; users should specify the edition used in `MicroephysCoordinateSystemDescription`.
+FranklinPaxinos:
+  value: FranklinPaxinos
+  display_name: Franklin-Paxinos
+  description: |
+    The Franklin and Paxinos mouse brain atlas (RRID:SCR_007127), a widely used stereotaxic coordinate system for the mouse brain.
+    Provides standardized coordinates based on skull landmarks (bregma, lambda) for targeting brain structures.
+    Reference: Franklin KBJ, Paxinos G. The Mouse Brain in Stereotaxic Coordinates. Academic Press.
+    Multiple editions available; users should specify the edition used in `MicroephysCoordinateSystemDescription`.
+SwansonRat:
+  value: SwansonRat
+  display_name: Swanson Rat
+  description: |
+    The Swanson rat brain atlas (RRID:SCR_007367), a widely used stereotaxic coordinate system for the rat brain.
+    Provides detailed cytoarchitectonic parcellation and standardized coordinates for targeting brain structures.
+    Reference: Swanson LW. Brain Maps: Structure of the Rat Brain. Elsevier.
+    Multiple editions available; users should specify the edition used in `MicroephysCoordinateSystemDescription`.
+CHARM:
+  value: CHARM
+  display_name: CHARM
+  description: |
+    Cortical Hierarchy Atlas of the Rhesus Macaque (RRID:SCR_023283), a modern MRI-based atlas for the macaque brain.
+    Provides hierarchical cortical parcellation based on anatomical connectivity patterns.
+    Reference: Jung B, Taylor PA, Seidlitz J, Sponheim C, Perkins P, Ungerleider LG, Glen D, Messinger A.
+    A comprehensive macaque fMRI pipeline and hierarchical atlas. NeuroImage. 2021;235:117997.
+    [doi:10.1016/j.neuroimage.2021.117997](https://doi.org/10.1016/j.neuroimage.2021.117997).
+D99:
+  value: D99
+  display_name: D99
+  description: |
+    Digital version of the Saleem and Logothetis macaque brain atlas (RRID:SCR_014606).
+    Provides detailed parcellation of the rhesus macaque brain based on histological sections.
+    Reference: Reveley C, Gruslys A, Ye FQ, Glen D, Samaha J, Russ BE, Saad Z, Seth AK, Leopold DA, Saleem KS.
+    Three-Dimensional Digital Template Atlas of the Macaque Brain. Cereb Cortex. 2017;27(9):4463-4477.
+    [doi:10.1093/cercor/bhw248](https://doi.org/10.1093/cercor/bhw248).
+PaxinosMacaque:
+  value: PaxinosMacaque
+  display_name: Paxinos Macaque
+  description: |
+    The Paxinos rhesus macaque brain atlas (RRID:SCR_016249), a stereotaxic coordinate system for the macaque brain.
+    Provides standardized coordinates based on stereotaxic landmarks for targeting brain structures.
+    Reference: Paxinos G, Huang XF, Petrides M, Toga AW. The Rhesus Monkey Brain in Stereotaxic Coordinates. Academic Press.
+    Multiple editions available; users should specify the edition used in `MicroephysCoordinateSystemDescription`.
+MarmosetBrainAtlas:
+  value: MarmosetBrainAtlas
+  display_name: Marmoset Brain Atlas
+  description: |
+    A standardized 3D coordinate system for the common marmoset brain (RRID:SCR_023286).
+    Provides high-resolution anatomical reference for marmoset brain studies.
+    Reference: Liu C, Ye FQ, Yen CC, Newman JD, Glen D, Leopold DA, Silva AC.
+    A digital 3D atlas of the marmoset brain based on multi-modal MRI. NeuroImage. 2018;169:106-116.
+    [doi:10.1016/j.neuroimage.2017.12.004](https://doi.org/10.1016/j.neuroimage.2017.12.004).