3d density heat map analysis  (Amira Pharmaceuticals)

Journal: Brain

Article Title: A ventral glomerular deficit in Parkinson’s disease revealed by whole olfactory bulb reconstruction

doi: 10.1093/brain/awx208

Figure Lengend Snippet: Invasive glomeruli. ( A ) Immunofluorescence of a horizontal section of the olfactory bulb from normal Case OFB42 with antibodies against VGLUT2 and NCAM. Some glomeruli (arrows) protrude well below the inner boundary of the glomerular layer (grey dotted line). The outer boundary of the glomerular layer (white dotted line) is adjacent to the olfactory nerve layer, which is at the surface of the bulb. ( B–F ) 3D reconstruction of normal Case OFB42. Glomerular voxels are rendered in green, and examples of invasive glomeruli in red. A view of the dorsal surface ( B ) demonstrates dense glomerular coverage toward anterior but not posterior. A slightly slanted view ( C ) showing the anterior-ventral-lateral surface provides a view of invasive glomeruli between gaps of superficial glomeruli. A view of the ventral surface ( D ) demonstrates that glomerular coverage extends ventrally much further toward posterior compared to dorsally. By only showing glomerular voxels midway along the anterior-posterior axis ( E ), the deep location of the invasive glomeruli can be fully appreciated when viewed from anterior ( F ). ( G ) Immunofluorescence image from normal Case OFB48 depicting structures (arrows) with the immunohistochemical characteristics and typical morphology of glomeruli, and located outside the glomerular layer. ( H ) Immunofluorescence image from normal Case OFB48 depicting atypical structures such as stalks of axons with small glomeruli (left-facing arrows) and branching patterns or tangles of axons (right-facing arrow). ( I ) Immunofluorescence image from normal Case OFB43 depicting a hybrid structure (arrow), which resembles a conventional glomerulus toward the olfactory nerve layer but resembles a linear tangle toward the external plexiform layer.

Article Snippet: The 3D density heat map analysis was performed on segmented glomerular datasets in Amira.

Techniques: Immunofluorescence, Immunohistochemical staining

Journal: Brain

Article Title: A ventral glomerular deficit in Parkinson’s disease revealed by whole olfactory bulb reconstruction

doi: 10.1093/brain/awx208

Figure Lengend Snippet: Quantification of invasive glomeruli. ( A ) Cross-section images of a 3D mask with bins defined by the distance of each glomerular voxel from the nearest surface. ( Top ) Lateral view of such a 3D mask that was cut along the anterior-posterior (a–p) and dorsal-ventral (d–v) axes at a point halfway on the medial-lateral axis, representing a sagittal view on a virtually-cleaved olfactory bulb. ( Bottom ) Dorsal view of the 3D mask that was cut along the anterior-posterior and medial-lateral axes halfway along the dorsal-ventral plane, representing a horizontal view on a virtually-cleaved olfactory bulb. ( B and C ) 3D rendering of the glomerular voxels from Cases OFB48 and PD50 with a colour gradient indicating the depth of each glomerular voxel. The gradient extends from superficial (blue) to deep (red). The rendering of normal Case OFB48 ( B ) reveals mostly blue and green voxels, indicating that the vast majority of glomerular voxels are near the surface. The high abundance of red voxels inParkinson’s disease Case PD50 ( C ) indicates that there are numerous glomerular voxels deep within the olfactory bulb. ( D ) Plots of the abundance of glomerular voxels along the surface-to-core dimension. The y -axis is normalized to be proportional for each olfactory bulb, such that the area below a curve amounts to 100% of the glomerular voxels for a given olfactory bulb. The x -axis is normalized to the distance from the surface to the core along 10 bins. The core is defined as the point that is the furthest from all surfaces of the olfactory bulb. ( E ) The profiles in D were averaged between the two categories of samples [normal versus Parkinson’s disease, (PD)] and plotted. Error bars are standard error of the mean (SEM).

Article Snippet: The 3D density heat map analysis was performed on segmented glomerular datasets in Amira.

Techniques:

Journal: Brain

Article Title: A ventral glomerular deficit in Parkinson’s disease revealed by whole olfactory bulb reconstruction

doi: 10.1093/brain/awx208

Figure Lengend Snippet: Profiling glomeruli in normal and Parkinson’s disease cases. 3D reconstructions from section series spanning entire olfactory bulbs from normal and Parkinson’s disease cases. Individual glomeruli are labelled in confetti-like colours. ( A ) The surface of normal Case OFB48 is densely permeated with glomerular voxels, both dorsally and ventrally. Glomerular voxels on the dorsal surface are restricted toward anterior ( left ). The ventral aspect exhibits a high density of glomerular voxels from anterior to posterior (from left to right ). ( B ) The glomerular voxels in Parkinson’s disease Case PD42 are relatively sparse, with comparable density and incidence along the dorsal and ventral surfaces on the bulb. ( C ) The GGVV in mm 3 was calculated by summing all segmented glomerular voxels. Horizontal line indicates mean, bars indicate SEM; two-tailed t -test P = 0.0391.

Article Snippet: The 3D density heat map analysis was performed on segmented glomerular datasets in Amira.

Techniques: Two Tailed Test

Journal: Brain

Article Title: A ventral glomerular deficit in Parkinson’s disease revealed by whole olfactory bulb reconstruction

doi: 10.1093/brain/awx208

Figure Lengend Snippet: Distribution of glomerular voxels in normal and Parkinson’s disease cases. ( A ) Segmented 3D datasets of olfactory bulbs were converted into virtual coronal sections. The coronal sections were subdivided into eight segments, and the fraction of glomerular voxels within each segment was computed. The two groups (Parkinson’s disease and normal) show a differential distribution of glomeruli among these octants ( n = 11 olfactory bulbs). ( B ) Plotting the percentage of glomerular voxels in the ventral and dorsal halves of the olfactory bulb against the GGVV shows significant differences between Parkinson’s disease cases (red) and normal cases (blue). ( C ) Density heat maps visualize the density of glomerular voxels on the 3D reconstruction of an olfactory bulb, by pseudocolouring each glomerular voxel according to how many glomerular voxels are found within a 300 -µm radius. Normal Case OFB48 is densely covered with glomerular voxels ventrally but has few glomerular voxels dorsally. Parkinson’s disease Case PD50 has a few hotspots dorsally, and overall glomerular voxels are more evenly distributed compared to in Case OFB48. Normal Case OFB43 has many glomerular voxels ventrally, but few on the sides and is less densely covered dorsally.

Article Snippet: The 3D density heat map analysis was performed on segmented glomerular datasets in Amira.

Techniques: