CAF dataset for  Allen Reference Atlas

The following description is related to Allen Reference Atlas CAF dataset available with the following links: live preview, dataset details. The CAF dataset was created by Łukasz Wałejko and Piotr Majka.

Detailed description of volume preprocessing:

1. Fetch AtlasAnnotation25.sva sparse volume file from  ABA Website.
2. Coordinates in this volume are expressed in  Mouse_ABAvoxel_1.0 (ABAvoxel, INCF:0100) SRS, in which units of measurements are voxels. In order to express data in stereotaxic coordinates (with bregma point as origin of the coordinate system), the volume has to be transformed into  Mouse_ABAreference_1.0 SRS (ABAreference, INCF:0101).

3. Such transformation is given by the  TransfomPOI INCF DAI service (ie.  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 the following equation:

After all transformations, matrix M reads:

M=
[[  2.71693750e-02  -8.17542750e-05  -5.01197500e-04  -1.25701700e+00]
 [  8.92628250e-04   2.82020000e-02  -2.71143000e-04  -1.28628500e+00]
 [ -5.86774750e-04  -8.96920500e-04  -2.59281250e-02   6.04778000e+00]
 [  0.00000000e+00   1.73472348e-18   0.00000000e+00   1.00000000e+00]]

and M':

M'=
[[  1.00000000e+00  -2.89888217e-03  -1.93302640e-02  -1.25701700e+00]
 [  3.28542063e-02   1.00000000e+00  -1.04574858e-02  -1.28628500e+00]
 [ -2.15969175e-02  -3.18034359e-02  -1.00000000e+00   6.04778000e+00]
 [  0.00000000e+00   6.15106544e-17   0.00000000e+00   1.00000000e+00]]

Then, an initial volume from AtlasAnnotation25.sva is transformed using M' and the resulting volume is used by the 3dBAR parser to create CAF dataset.

Below you may find comparison of brain outlines created using raw volume (dark gray) and volume after transformation (light gray):