Visualizing Nerve Cells in a Section of Rat Cerebellum

The montage datasets are from images of nerve cells in a section of rat cerebellum produced by a laser scanning confocal microscope.

The process generates multiple sub-volumes where each sub-volume represents a section of the nerve slice sample. These sub-volumes are mosaiced together to produce the entire volume.

Montage 1

Individual Sub-volumes

The "Montage 1" dataset consists of 18 individual sub-volumes arranged into four rows and five columns. Each sub-volume consists of a stack of 40 images slices. Each image slice is a 512x512 resolution 24-bit RGB image. The total dataset size is 540 MBytes.


Sub-volume 1	Sub-volume 2	Sub-volume 3	Sub-volume 4	Sub-volume 5


Sub-volume 6	Sub-volume 7	Sub-volume 8	Sub-volume 9	Sub-volume 10

Combined Volume

The sub-volumes are mosaiced in the XY-plane to form a single volume. The edges of adjacent sub-volumes overlap by about 20%. The exact overlap (in pixels) between adjacent sub-volumes needs to be provided along with each dataset. This information was not available, so I used 102 pixel overlap as an estimate.

Volume rendering

Frames

Once the entire volume was rendered, it was possible to render the volume from various viewpoints.


Frame 150	Frame 200	Frame 250	Frame 300

Fly-thru Animations

The frames can be sequenced to simulate a fly-thru of the entire volume.

Quicktime Animation: (268 x 218) (350 frames) (27 MB)

Quicktime Animation: (536 x 436) (350 frames) (90 MB)

Montage 2

Individual Sub-volumes

The "Montage 2" dataset cosists of 9 individual sub-volumes arranged into three rows and three columns. Each sub-volume consists of a stack of 51 images slices. Each image slice is a 512x512 resolution 24-bit RGB image. The total dataset size is 344 MBytes.


Sub-volume 1	Sub-volume 2	Sub-volume 3


Sub-volume 4	Sub-volume 5	Sub-volume 6


Sub-volume 7	Sub-volume 8	Sub-volume 9

Combined Volume

Volume rendering

Frames

Once the entire volume was rendered, it was possible to render the volume from various viewpoints.


Frame 150	Frame 200	Frame 250	Frame 300

Fly-thru Animation

The frames can be sequenced to simulate a fly-thru of the entire volume.

Quicktime Animation: (333 x 333) (350 frames) (22 MB)

Credits:

M. Martone, S. Peltier
NCMIR, University of California, San Diego

A. DeCastro, D. Nadeau
San Diego Supercomputer Center, University of California, San Diego