CAF dataset for [http://mouse.brain-map.org/launchviewer.do Allen Reference Atlas]:

  1. Fetch `AtlasAnnotation25.sva` sparse volume file from [http://community.brain-map.org/confluence/download/attachments/525267/data.zip?version=1 ABA Website].
  2. Coordinates in this volume are expressed in  [http://incf-dev.crbs.ucsd.edu/aba/atlas?service=WPS&version=1.0.0&request=Execute&Identifier=ListSRSs Mouse_ABAvoxel_1.0] (`ABAvoxel, INCF:0100`) SRS, in which units of measurements are voxels. In order to express coordinates in stereotaxic coordinates (with bregma point defined as origin of the coordinate system), the volume has to be transformed into [http://incf-dev.crbs.ucsd.edu/aba/atlas?service=WPS&version=1.0.0&request=Execute&Identifier=ListSRSs Mouse_ABAreference_1.0] SRS (`ABAreference, INCF:0101`).

  3. Such transfomration is given by the [http://code.google.com/p/incf-dai/wiki/AtlasRequestInterfaceSpec#TransformPOI TransfomPOI] INCF DAI service (ie. [http://incf-dev.crbs.ucsd.edu/aba/atlas?service=WPS&version=1.0.0&request=Execute&Identifier=TransformPOI&DataInputs=transformationCode=Mouse_ABAvoxel_1.0_To_Mouse_ABAreference_1.0_v1.0;x=1;y=112;z=162 this] request).

  4. Tranformation may be calculated from 4 points in `ABAvoxel` SRS (`p1,p2,p3,p4`) and 4 corresponding point in `ABAreference` SRS (`p1',p2',p3',p4'`) by solving following equation: