Mouse - Waxholm Space delineation 2009

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Credits & Links

• 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 rcho sequence, using TR=50 ms and TE=4.3 ms.
  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.
  Use the MBAT toolkit to see 3D renderings of the data sets and to register your own data to it.
• The Scalable Brain Atlas is created by Rembrandt Bakker and Gleb Bezgin, under supervision of Rolf Kötter
  in the NeuroPhysiology and -Informatics group of the Donders Institute, Radboud UMC Nijmegen.