3-D rendering of MCell simulation output can be performed
with the following imaging software packages (cf. the MODE statement in the VIZ_DATA_OUTPUT block of MCell's MDL):
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(1) IBM's DataExplorer
(open source, http://www.research.ibm.com/dx/);
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(2) Pixar's RenderMan (proprietary, http://www.pixar.com/);
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(3) rayshade (open source, ftp://graphics.stanford.edu/pub/rayshade/);
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(4) povray (open source, http://www.povray.org/);
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(5) irit
(open source, http://www.cs.technion.ac.il/~gershon/irit/irit_index.html).
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3D Reconstruction:
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| Voxtrace
(open source, http://www.ncmir.ucsd.edu/Downloads/Software/overview.htm) |
2D Plotting: |
| For 2-D plotting of large data sets from MCell's REACTION_DATA_OUTPUT
block(s), we recommend xmgrace
(open source, http://plasma-gate.weizmann.ac.il/Grace/). |
Finite element modeling of neurons:
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