Changes between Version 9 and Version 10 of barSoftwareParsersAba

Timestamp:

10/13/11 10:25:15 (13 years ago)

Author:

pmajka

Comment:

--

barSoftwareParsersAba

@@ -1 +1 @@
 == CAF dataset for [http://mouse.brain-map.org/launchviewer.do Allen Reference Atlas] ==
 
-'''The following description is related to Allen Reference Atlas CAF dataset available with following links: [http://www.3dbar.org:8080/getPreview?cafDatasetName=aba;structureName=Brain live preview], [http://www.3dbar.org:8080/getCafInfoPage?cafDatasetName=aba dataset details].'''
+'''The following description is related to Allen Reference Atlas CAF dataset available with the following links: [http://www.3dbar.org:8080/getPreview?cafDatasetName=aba;structureName=Brain live preview], [http://www.3dbar.org:8080/getCafInfoPage?cafDatasetName=aba dataset details].'''
 
 Detailed description of volume preprocessing:
 
   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 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`).
+  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 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 transformation 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]).