Update Installation.rst

Docs/Installation.rst

@@ -67,19 +67,27 @@ QuickNII can be used with the following reference atlases:
 |Waxholm Space Atlas of the Sprague Dawley rat v3  |
 |                                                  |
 |Waxholm Space Atlas of the Sprague Dawley rat v4  |
-+--------------------------------------------------+     
-How to cite:
++--------------------------------------------------+    
 
-* Allen Mouse Brain Atlas (@ 2004 Allen Institute for Brain Science. Allen Mouse Brain Atlas. Available from:  
-http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/annotation/).                     
+** How to cite:** 
 
-* Waxholm Space atlas of the Sprague Dawley rat brain       
-version 1.01,2,3 and 4 (RRID: SCR_017124; Papp et al.,NeuroImage 97, 374-386, 2014;
-Papp et al., NeuroImage 105, 561–562, 2015; Kjonigsen et al., NeuroImage 108, 441-449, 2015;
-Osen et al., NeuroImage 199, 38-56, 2019; Kleven et al., in preparation)                         
+**Allen Mouse Brain Atlas Common Coordinate Framework version 3 (RRID:JCR_020999 and RRID:JRC_021000)** 
 
-For reuse of the Waxholm Space atlas of the Sprague Dawley rat brain,see citation policy at  
-https://www.nitrc.org/citation/?group_id=1081
+* 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. Epub 2020 May 7. 
+
+See the `citation policy <https://alleninstitute.org/citation-policy/>`_ from the Allen Intitute for more information.
+
+**Waxholm Atlas of the Sprague Dawley Rat (RRID:SCR_017124)**
+
+Please refer to the atlas using RRID:SCR_017124, specify the atlas version(s) used, and cite the most recent publication:
+
+•	Kleven, H., Bjerke, I.E., Clascá, F. et al. Waxholm Space atlas of the rat brain: a 3D atlas supporting data analysis and integration. Nat Methods 20, 1822–1829 (2023). DOI: 10.1038/s41592-023-02034-3
+
+If your work makes use of previous atlas versions, or brain region descriptions detailed in earlier publications, please also cite the corresponding publication:
+
+•	Version 1: Papp EA, Leergaard TB, Calabrese E, Johnson GA, Bjaalie JG (2014) Waxholm Space atlas of the Sprague Dawley rat brain. NeuroImage 97, 374-386. DOI: 10.1016/j.neuroimage.2014.04.001
+•	Version 2: Kjonigsen LJ, Lillehaug S, Bjaalie JG, Witter MP, Leergaard TB (2015) Waxholm Space atlas of the rat brain hippocampal region: Three-dimensional delineations based on magnetic resonance and diffusion tensor imaging. NeuroImage 108, 441-449. DOI: 10.1016/j.neuroimage.2014.12.080
+•	Version 3: Osen KK, Imad J, Wennberg AE, Papp EA, Leergaard TB (2019) Waxholm Space atlas of the rat brain auditory system: Three-dimensional delineations based on structural and diffusion tensor magnetic resonance imaging. NeuroImage 199, 38-56. DOI: 10.1016/j.neuroimage.2019.05.016                        
 
 **Release notes**
 ~~~~~~~~~~~~~~~~~~