Example animations, Space software

Example Space Software animations

Human brain surface
Virion structure
Orthologia
3-D tiling
Mouse embryo
Ambiguous triple cube
Tritorus
Visual motor mapping
Knitted brain
Halley's egg
Brodmann brain
Huttenlocher graph
Baby brain
Hippocampi
Mushroom
Human V1 retinotopy, far periphery
Human hand and forearm CT
Human brain MRI slices
Human index finger joint
Owl head MRI

Also see Example Space Software renderings

Human brain surface

Human brain animation, blended with Brodmann area coloring

Brain_Brodmann_blend.swf 1.3 MB, 640 x 480 px.

Two rotations, one colored by Brodmann areas. Larger (1170 x 880 px.) individual frames of the "base" brain are available in a \brain_animations sub-directory.

rotating brain animation, rendered from Colin27T1

brain_colin27T1.avi 5 MB
brain_colin27T1_small_120x3.avi 1 MB

Stereo pair - cross view.
brain_colin27T1_stereo.avi 10 MB

Human brain, full rotation, from T1 weighted MRI, average of 27 scans (Colin, Montreal Neurological Institute). Also see High resolution, single frame, stereo pair and Brodmann coded still images.

Virion structure

P22 bacteriophage, virion structure animation

P22 bacteriophage virion animation thumbnail

emd_1222_slice_and_roll.swf 2.7 MB, 784 x 588 px.
emd_1222_slice_and_roll_c.avi 14 MB, 784 x 588 px.
A smaller GIF animation of the slices at left.

At left is a surface rendering, and at right 2-D slices along the axis.

P22 bacteriophage, virion structure renderings

P22 bacteriophage virion renderings thumbnail

emd_1222_rendered.jpg
(still image)

The virion of P22, a bacteriophage. A virion is the infectious form of a virus as it exists outside the host cell, consisting of a nucleic acid core, and a protein coat.

Rendered from a volumetric Cryo-EM (electon microscope) asymmetric reconstruction.
Data source: EMD_1222, Macromolecular Structure Database.

"The large bulb is the head capsid, containing the DNA injected into the host bacterium, which then commandeers the host cell, turning it into a virus factory. The symmetry of all head capsids of various bacteriophage is icosohedral, made up of large proteins woven together rather like a quilt.

In some cases, the icosohedral symmetry is a little twisted, with hexagonal units wrapped around edges instead of meeting at edges. The corners of the icosohedron are always pentagonal." Steve McQuinn

J.Chang, P.Weigele, J.King, W.Chiu, W.Jiang:
Cryo-EM asymmetric reconstruction of bacteriophage P22 reveals organization of its DNA packaging and infecting machinery. Structure (2006) 14, pp. 1073-1082 [PubMed entry 16730179]

Abstract: "The mechanisms by which most double-stranded DNA viruses package and release their genomic DNA are not fully understood. Single particle cryo-electron microscopy and asymmetric 3D reconstruction reveal the organization of the complete bacteriophage P22 virion, including the protein channel through which DNA is first packaged and later ejected. This channel is formed by a dodecamer of portal proteins and sealed by a tail hub consisting of two stacked barrels capped by a protein needle. Six trimeric tailspikes attached around this tail hub are kinked, suggesting a functional hinge that may be used to trigger DNA release. Inside the capsid, the portal's central channel is plugged by densities interpreted as pilot/injection proteins. A short rod-like density near these proteins may be the terminal segment of the dsDNA genome. The coaxially packed DNA genome is encapsidated by the icosahedral shell. This complete structure unifies various biochemical, genetic, and crystallographic data of its components from the past several decades."

Orthologia

Orthologia twist animation

Ortho_twist_640_640.swf 10 MB, 640 x 640 px.
Ortho_twist_640_480.wmv 7 MB, 640 x 480 px.

Othologia trispiralis Orthologia trispiralis

Orthologia_trispiralis.jpg
(still image)

Imaginary beast, a bugit, based on a similarity tiling of logarithmic spirals and the Thue-Morse sequence. Only assembly of the frames was done using Space Software.

3-D tiling

Vortex_apple_320x240.wmv Vortex_apple_640x480.wmv	Vortex_apple_triple_320x240.wmv Vortex_apple_triple_640x480.wmv	(still image)	(still image)
This shape, forms a (monohedral) tiling that fills space with an octahedral symmetry. (stereo pair, cross-view) Volume data: Vortex_apple.vol.gz	Three tiles (see image at left) interlinked to show how they are rotated and translated to fill space. (stereo pair, cross-view) Volume data: Vortex_apple_triple.vol.gz (1.5 MB)	A 3-D tiling, having a self-conjugate surface, based on tiles to left. (stereo pair touching at center, cross-view) Volume data: Violin_tiling.vol.gz	Same surface form, with different coloring, as the tiling to the right. (stereo pair, cross-view) Volume data: Vortex_tiling.vol.gz

A 3-D tiling based on a logarithmic spiral. The shapes are generated with Matlab, then colored and rendered with Space Software.
See Logarithmic spirals, waves, and tilings for spiral Matlab code and related logarithmic spirals, images and animations.

Mouse embryo

Mouse_embryo_rot.wmv 6 MB, 640 x 480 px., stereo pair - cross view
Mouse_embryo_rot.avi 36 MB, 856 x 642 px.
Mouse embryo, volume rendered from MRI data. Embryonic age is 23 days after conception.
Raw volume data available from Caltech Atlas of Mouse Development (data © California Institute of Technology, Pasadena).

Ambiguous triple cube

3 segment rocking. (Best if viewed as a continuous loop/repeat.)
Ambiguous_Triple_Cube_small.avi 3.4 MB, 423 x 456 px.
Ambiguous_Triple_Cube.avi 12 MB, high resolution version: 846 x 912 px.

8 segment rotation, cropped. (Best if viewed as a continuous loop/repeat.)
Ambiguous_Triple_Cube_x2rHc320.wmv 2 MB, 320 x 240 px., 32 s
Ambiguous_Triple_Cube_x2rHc640.wmv 8 MB, high resolution version: 640 x 480 px., 32 s

Motion resolves the depth ambiguities, but there are depth discontinuities at motion transitions. The discontinuities aren't apparent until sometime after the transitions, so the percept is smooth. This visual illusion is derived from Oscar Reutersvärd's "Impossible Triangle", which was popularized in the 1950's by Roger Penrose, and is sometimes called a "Penrose Triangle".
My percept of the "rocking" version is different than the "rotating" version: in the rotating version I often percieve the cubes to apparently slide, or bounce, to their new configuration.
Larger still image: Ambiguous_Triple_Cube.jpg
Rendered from a chunk of Digital Morphology CT data of Quercus robur (English or Peduncate Oak): Dr. Peter Gasson, 2002, "Quercus robur" (On-line), Digital Morphology. Accessed October 23, 2006 at http://digimorph.org/specimens/Quercus_robur/. Volume data for the cube: Oak_cube.vol.gz (8 MB).

Tritorus

tritorus_ortho_80_20_rotation.avi 3.5 MB, stereo pair - cross view

tritorus_ortho_80_20_slices.avi 4 MB
Sequential slices along the axis of rotational symmetry.

Three mutually linked and mutually orthogonal tori in an othogonal configuration. Here's tritorus_80_20.vol.gz, the volume they were rendered from. Also see rendered image along axis of rotational symmetry, This is not an image of a trefoil knot.

tritorus_60_19_rotation.avi 4 MB, stereo pair - cross view
Near maximal radii linking tori in a linear 120 degree rotation configuration. Here's tritorus_60_19.vol.gz, the volume they were rendered from, and torus_60_19.vol.gz, a single torus volume.

Visual motor mapping

Functional MRI retinotopy and motor strip mapping.

FMRI_VisMotSystems_640.avi
50 MB (Warning: large file)
FMRI_VisMotSystems_320.avi
30 MB, half size frames

FMRI_VisMotSystems_640.wmv
13 MB

Functional MRI retinotopy and motor strip mapping. (Visual system artwork and animation by Greg Scott). Compositing and artwork done with Premier software.

Knitted brain

(still image)

(composite still image: fabric, MRI fabric, MRI human, stained slice human)

The_Knitted_Brain_composite.avi 7 MB
Rendered MRI of a knitted brain by Karen Norberg (see Karen Norberg #1), a gorgeous fabric sculpture. The sculpture is zippered at corpus collosum, allowing exposure of internal brain structures. The sculpture was soaked with water before scanning (by Scott Watrous) with a 3-D FLASH sequence. THESE IMAGES ARE COPYWRITED BY KAREN NORBERG, DO NOT USE WITHOUT EXPLICIT WRITTEN PERMISSION.

Haley's egg

Haleys_egg_cutaway.avi .5 MB
Rendered strips on the surface of an ellisoid, after Haley Engle's sketch. Volume data constructed using simple Space "pen" operations.
Here's the raw volume (.vol, .5 MB), and a higher resolution rendered image

Brodmann brain
Rendered brain color coded by Brodmann area.

Brodmann_brain_movie.avi 8 MB
Rendered brain color coded by Brodmann area.

Huttenlocher graph
animated chart of synaptic development after Huttenlocher

animated chart of synaptic development after Huttenlocher

Huttenlocher_composite.avi 8 MB
Huttenlocher_visual.avi
Huttenlocher_auditory_frontal.avi
Animated chart of synaptic development after Huttenlocher.

sequential highlight of visual, auditory, prefrontal Brodmann areas

sequential highlight of visual, auditory, prefrontal Brodmann areas

Highlight_brodmann_regions.avi 5 MB
Sequential highlighting of visual, auditory, prefrontal Brodmann areas.

Baby brain

Baby_brain.avi 5 MB
Cartoon fade from child to rendered brain to Brodmann areas.
Baby_brain_2.avi 7 MB
Slow fade to and from brain.

Brodmann visual cortex

Brodmann_visual_test.avi 1.2 MB
Context of visual cortex within brain, cartoon.

Hippocampi
six pairs of hippocampi, segmented from MRI

Hippocampi_six_pairs.avi 3.5 MB
Rendered hippocampus segmentations from T1weighted MR images, six human subjects.

Mushroom
mushroom, MRI

mushroom_12.avi .8 MB
mushroom, MRI

Point_cloud.gif .4 MB
Manually marked tagged neurons from serial microscopy, cuttlefish brain.

faces_gray.gif .3 MB
faces_gray.avi .2 MB
Example stimuli movie (no ISI) in LeGrand, Maurer, Brent Nature Neuroscience, Vol 6, No 10, Oct 2003 paper.
top: feature differences, middle: contour differences, bottom: relative position differences.

Human V1 retinotopy, far periphery

V1_upper_right_far_periphery.avi 24 MB
Statistical maps overlaid on medial sagital slices of occipital pole through V1. Single subject, individual 8 Hz flashing stimuli across a range of eccentricities, 2 to 78 degrees.

Human hand and forearm CT

Hand_CT_anim_1.gif 2.8 MB
Hand_CT_anim_1.avi 1.5 MB
Human hand, rendered stereo surface, rendered bone, from CT.

rotating_hemi.gif 3.5 MB
rotating_hemi.avi 1.4 MB
Human brain hemisphere, rendered surface from T1 weighted MRI.

rotating_brain.gif 5.4 MB
rotating_brain.avi 2.0 MB
Human head, surface rendered brain full rotation, from T1 weighted MRI.

Human brain MRI slices

orthogonal_slices.gif 4.0 MB
orthogonal_slices.avi 2.0 MB
Human brain, three orthogonal T1 weighted MRI slice sets.

sagital_slices.gif 1.3 MB
sagital_slices.avi .6 MB
Human brain, sagital T1 weighted MRI slices.

coronal_slices.gif 1.3 MB
coronal_slices.avi .6 MB
Human brain, coronal T1 weighted MRI slices.

axial_slices.gif 1.1 MB
axial_slices.avi .6 MB
Human brain, axial (transverse) T1 weighted MRI slices.

slice_twice.gif 7.4 MB
slice_twice.avi 2.9 MB
Human head, surface rendered brain and slices in axial and coronal direction, from T1 weighted MRI.

rotate_and_slice.gif 10 MB
rotate_and_slice.avi 4.1 MB
Human head, surface rendered brain full rotation and slices in axial and coronal direction, from T1 weighted MRI.

Human index finger joint

joint_movie_1.gif 4.0 MB
joint_movie_1.avi 1.9 MB
Human index finger joint, rendered stereo surface, rendered bone segmentation, from T1 weighted MRI.

Owl head MRI

owl_T2_movie_1.gif 4.0 MB
owl_T2_movie_1.avi 1.8 MB
Barn owl head, rendered stereo surface of brain and eyes, from T1 weighted MRI.

cuttlefish_example_sections.gif 1.3 MB
Cuttlefish brain (posterior lobe?), MIP of serial microscopy sections with tagged neuron markers.

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There are no restrictions on use of the images and animations on this page. Claiming to be the originator of the material, explicitly or implicitly, is bad karma. A link (if appropriate), a note to dow[at]uoregon.edu, and credit are appreciated but not required.

Comments are welcome (dow[at]uoregon.edu).