Mouse - Waxholm Space delineation 2012

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About this atlas

The template name WHS12 refers to Waxholm space 2012. The region parcellation has version number 0.6.1 (source), with region abbreviations taken from the NeuroNames ontology 2012, except for those in between square brackets.

The Waxholm space is a coordinate-based reference space for the mapping and registration of neuroanatomical data in the mouse brain.
See Johnson et al, Neuroimage. 2010 Nov 1;53(2):365-372 for a detailed account of its goals, procedures, and available data in the original, full resolution.

The three MR image modalities were acquired as follows:

• All scans were performed on a 9.4 T vertical bore magnet interfaced to a GE console running Epic 12.4X (GE Medical Systems, Milwaukee, WI).
• The T1 ('spin lattice relaxation') data was acquired with an RF refocused spin echo sequence, using TR=50 ms and a TE=5.1 ms.
• The T2 ('spin spin relaxation') data was acquired with a Carr-Purcell-Meiboom-Gill (CPMG) multi-echo sequence, with TR=300 ms and TE ranging from 7.5 to 60 ms.
• The T2* ('magnetic susceptibility') data was acquired with a 45° gradient echo sequence, using TR=50 ms and TE=4.3 ms. An affine transform is applied to the raw T2 and T2* scans to best align with the T1 (CIVM datasets CT2Warped2T1.nii and CT2starWarped2T1.nii).

The NISSL data is the result of conventional histology: frozen brains were cut into 21 µm horizontal slices, stained for Nissl substance, and photographed at 9.9 µm resolution.

The defining citations for this atlas template are:

1. Johnson GA, Badea A, Brandenburg J, Cofer G, Fubara B, Liu S, Nissanov J (2010) "Waxholm space: an image-based reference for coordinating mouse brain research." Neuroimage 53(2):365-72. [doi 10.1016/j.neuroimage.2010.06.067]

• T1: T1 MRI with TR=50 ms and a TE=5.1 ms
  • ../../templates/WHS12/source/canon_T1_r_downsample2.nii.gz; filesize 57444 kB; shape [256x512x256]
• T2: T2 MRI with TR=300 ms and TE ranging from 7.5 to 60 ms
  • ../../templates/WHS12/source/CT2Warped2T1_downsample2.nii.gz; filesize 48283 kB; shape [256x512x256]
• T2*: T2* MRI with a 45° gradient echo sequence, TR=50 ms and TE=4.3 ms
  • ../../templates/WHS12/source/CT2starWarped2T1_downsample2.nii.gz; filesize 50477 kB; shape [256x512x256]
• labels: Region parcellation version 0.6.1
  The label index mapper converts label indices to acronyms, full names, and rgb-values.
  • ../../templates/WHS12/source/WHS_0_6_1_Labels_downsample2.nii.gz; filesize 833 kB; shape [256x512x256]
• coronal_svg: Coronal sections of the label volume "WHS_0_6_1_Labels.nii", converted to Scalable Vector Graphics.
  Brain regions are color-coded by the RGB to Acronym map, which can be chained with the Acronym to Fullname map.
  • ../../templates/WHS12/source/coronal_svg.zip; filesize 3273 kB
• wholebrain_mesh: surface mesh of the entire brain
  • ../../templates/WHS12/wholebrain.x3d; filesize 4422 kB