Mark Dow
Space Software
Geek art

Example Space Software renderings

    Also see Example Space Software animations.

Quail chick rendered from MRI, link to Quail and human visual hardware, link to Four knot 1, link to virion structure rendering, link to axial MRI slices of various contrasts, link to axial MRI slices of various contrasts, link to axial MRI slices of various contrasts, link to axial MRI slices of various contrasts, link to axial MRI slices of various contrasts, link to Volume rendering of the Visible Woman's head, link to Mouse embryo, link to Ambiguous Triple Cube, link to Knot a trefoil, link to human brain, rendered from Colin27T1, link to

3-D spiral tiles

Quail chick, MRI

     Quail chick, volume rendered from MRI data. Coturnix japonicus, embryonic age 10 days, ex ovo.

Quail chick surface rendering from MRI, link to
(stereo pair, cross view)

    Raw volume data available from Caltech Atlas of Quail Development (data © California Institute of Technology, Pasadena).

Quail and human vision hardware

    Comparison of MRI slices through the optic nerves of a quail chick and an adult human, scaled so the slice areas are about equal.
Quail and human visual hardware, link to
    The optic nerves of all vertebrates cross at the optic chiasm, at midline behind the eyes near the mid-brain structures.

    The zipper-like structure extending into the quail eye is a mystery to me. It appears to be an extension of the optic nerve into the retina (or what the retina develops from), but I've never seen an illustration of vertebrate eye development that shows anything like it. Another view of its structure can be seen in this surface rendering of the inside of the eyeball.

    Exterior surface rendering and information about the quail chick data.
    Information and volume data of human (me).

Four Knot 1

    A 2-D Thue-Morse pattern where the symbols are replaced by a motif that visually connects all adjacent symbols. The result is a woven pattern, with each "strand" forming a simple closed loop. Only the motif was constructed and rendered with Space Software.

Four knot 1 motif
The two square motifs, side-by-side, where each motif is a pi/2 rotation of the other.

Thue-Morse with Four knot motif algorithm graphic
The recursive replacement system that results in the 2-D Thue-Morse pattern.
 oblique view of the Four knot motif, link to Oblique viewpoint rendering of the 3-D motif used to construct Thue-Morse chain images. (Stereo pair, cross-view.)

Constructed and rendered using a single chiral spline segment, rotated/mirrored four times. (Credit to Greg Scott for writing the spline code.)

curveA_b_4.vol.gz (2 MB)		 Four knot 1 uncolored pattern, link to
The Thue-Morse tiling.		 Four knot 1, link to
The pattern after a pi/4 rotation and coloring of connected elements -- only those elements that are closed on this portion of the potentially infinite tiling.
  Matlab command (for the Thue-Morse tiling of this motif pair):
>> nimOut = L_system_tiling( 'TM', 4, 2, 1, 0, 'Chain_bc_motif_thumbnail.jpg', 0, [0 1; 1 0], [1 0; 0 1] );

    Why this works (nested circuits in this weave pattern, colored by connectivity in the left image) is a mystery to me. How would a larger Thue-Morse pattern with the same motifs be connected? I designed the motif, shading and coloring, but I didn't design the pattern; I found it.



Virion structure

    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.
P22 bacteriophage, virion structure renderingsP22 bacteriophage virion renderings, link to
emd_1222_rendered.jpg

(stereo pair, cross-view)
 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.
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."



3-D spiral tiles

    A 3-D tiling based on a logarithmic spiral. See Logarithmic spirals, waves, and tilings for spiral Matlab code and related logarithmic spirals, images and animations.
 3-D logarithmic spiral tiling, violin 3-D logarithmic spiral tiling, vortex 3-D logarithmic spiral tile 3 interlinked 3-D logarithmic spiral tiles
A 3-D tiling, having a self-conjugate surface, based on logarithmic spirals.
(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		 Disected element of the tiling to the right. This shape, forms a (monohedral) tiling that fills space with an octahedral symmetry.
(stereo pair, cross-view)

Rotation movie:
Vortex_apple_320x240.wmv
Vortex_apple_640x480.wmv

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)

Rotation movie:
Vortex_apple_triple_320x240.wmv
Vortex_apple_triple_640x480.wmv

Volume data:
Vortex_apple_triple.vol.gz (1.5 MB)


Mouse embryo

        Mouse embryo, volume rendered from MRI data. Embryonic age is 23 days after conception.
Mouse embryo, link to
Mouse_embryo_1a.jpg
(stereo pair, cross view)

    Also see animated rotation.
    Raw volume data available from Caltech Atlas of Mouse Development (data © California Institute of Technology, Pasadena).


Oak cubes

    Various arrangements of a volume rendered cube from high resolution CT of a chunk of oak. Also see more (similar) patterns at Oak cubes and hexagonal tilings and  Ambiguous Triple Cube animations.
Ambiguous Triple Cube, link to
Ambiguous_Triple_Cube.jpg

This form of ambiguity 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".		 48 Meta-cube
48_Meta-Cube_o4.jpg  (small)
48_Meta-Cube.jpg  (4 MB, 4900x4900 px.)

A shaded tesselation of cubes. This figure is composed of all rotations (3x8 corners), including mirroring (x2), of the same cube. In this sense it is a representation of the rotation group: in mechanics and geometry, the rotation group is the group of all rotations about the origin of 3-dimensional Euclidean space R3 under the operation of composition.
 16 Rotation abmbiguous cubes
16_Rotation_Ambiguous_Cubes_xp4.jpg  (medium)
16_Rotation_Ambiguous_Cubes_o10.jpg  (small)
16_Rotation_Ambiguous_Cubes.jpg  (large)
Rendered from DigiMorph 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).


Knot a trefoil

    Three mutally linked and mutually orthogonal tori.
Knot a trefoil, link to
tritorus_ortho.jpg

    This is not an image of a trefoil knot. See tritorus_ortho_80_20_rotation.avi (3.5 MB) and tritorus_ortho_80_20_slices.avi (4 MB) for other viewpoints.


Human brain, Brodmann areas

    A human brain volume rendered from T1 weighted MRI, an average of 27 scans (Colin27, Montreal Neurological Institute) and its conjunction with Brodmann areas (colored, at right). Stereo pairs, different combinations of same renderings.
human brain, rendered from Colin27T1, link to





Schematic set of neurons (crossed stereo pair).
neurons_43a_sh.jpg
Schematic set of neurons (crossed stereo pair).


Filtered depth map of colin24 brain.
bcolin24_chips.jpg
Filtered depth map of colin24 brain.


Tetrahedral gasket.
Tetra_5_oversampled8x.jpg
A fifth order Sierpinski tetrahedron. The Matlab function that generated the volume that this image is rendered from is cubic_manifold_general.m, hardcoded for this particular "fractal sponge".


High resolution surface rendering of T1 weighted MRI of head.
dow_MRI_big_head.jpg
High resolution surface rendering of T1 weighted MRI of head.


Rendered brain color coded by Brodmann area.
Brodmann_brain.jpg
Rendered brain color coded by Brodmann area.


Chart showing synaptic (density) development, after Huttenlocher.
Huttenlocher_composite.jpg
Chart showing synaptic (density) development in three brain regions, after Huttenlocher.

Axial MRI head slices, variety of image contrasts

    Axial MRI image of the same human head, at about the same plane, with five different contrasts.
axial MRI of human head, 5 different image contrasts
095_multi_modal_axial.jpg
The left pair used a T1 contrast MRI sequence designed to optimized contrast between white and gray matter. The two differ in suppression of the fat signal, most noticeable in the subcutaneous tissue on the outside of the skull. The third and fourth used T2 contrast. The third is a gradient echo-planar (EPI) image, with a T2 contrast sequence used in functional imaging due to it's sensitivity to the T2* component; blood oxygenation differences result in T2* variations through time.


Visisble Woman head, rendered

    Volume rendering of the Visible Woman's head.
Volume rendering of the Visible Woman's head, link to
Visible_Woman_head_rendered.jpg




Segmentation_flow_1.jpg



periph_act.jpg



owl_T2_sag.jpg
 t


gasket.jpg
A Menger sponge rendering.



cubic_cross_1_copy_rendered.jpg



CT_head_skin_threshold_axial_2.jpg



CT_head_skin_threshold.jpg



bJC_T1_smooth_white_oblique.jpg



bJC_T1_smooth_white.jpg



Age_range_composite.jpg  .7MB



000001_LR_render_1.jpg



000001_LR_ortho_slice_1.jpg



000001_LR_FFG_composite.jpg


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