BrainRAT HandBook

List of Figures

1.1. (Left) 3-D reconstruction of cresyl violet-stained sections clearly outlines the superior colliculus. (Right) The corresponding 3-D reconstruction of autoradiographic images indicates the extent of the metabolic activation during checkerboard stimulation in a control C57BL/6 mouse with one eye shut and one eye open.

1.2. 3-D reconstruction of the left and right manually segmented superior colliculus. The automatic extraction of the "activated" volume using the threshold method is represented in red and the symmetric volume in green.

1.3. Brain area (the superior colliculus) in which CMRGlu was significantly higher or lower in visually stimulated hemibrains than in the corresponding control hemibrains automatically detected by a voxel-wise statistical analysis. Significance is indicated with t statistic color scales, corresponding to the level of significance at voxel level.

1.4. Anatomo-functional superimposition and 3D reconstruction of the olfactory bulb.

1.5. 3D postmortem imaging of radioligand distribution in mouse brain after injection of [¹⁸F]-MPPF. Background black and white anatomic volumetric reconstruction of cresyl violet-stained sections shows bilateral location of 5-HT1A binding in mouse hippocampus. Pseudocolored digitized autoradiographs illustrate level of [¹⁸F]-MPPF binding and are color-coded from low (blue) to high (red) binding.

3.1. 3D reconstruction of histological volume (Nissl stain) encompassing a large part of the visual system (between bregma -5.2 mm and bregma -8.2 mm), in coronal, axial and sagittal views before (top) and after registration (bottom).

3.2. 3D reconstruction of [¹⁴C]-2DG autoradiographic volume, encompassing a large part of the visual system (between bregma -5.2 mm and bregma -8.2 mm), in coronal, axial and sagittal views before (top) and after registration (bottom).

3.3. All possible section arrangements on glass slides according to column first, which are managed by BrainRAT process 02. image - individualizing and stacking multiple slices.

3.4. All possible section arrangements on glass slides according to line first, which are managed by BrainRAT process 02. image - individualizing and stacking multiple slices.

3.5. Vertical (a) and horizontal (b) overlaps between two histological sections.

3.6. (a) Acquisition of autoradiographic sections and corresponding radioactive [¹⁴C] standards. (b) Acquisition of homologous histological stained sections.

3.7. Arrangement of glass slides on the surface of the scanner: Top->Bottom and Bottom->Top.

3.8. (a) Overall scan of histological sections stained with cresyl violet (three glass slides arranged in a column, 600 dpi). (b) Overall scan of corresponding [¹⁴C]-2DG autoradiographic sections. (c) Radioactive [¹⁴C] standards.