VolumeJ - example renderings

VolumeJ is part of the Bio-medical Imaging in Java site.

The following images are "not published", and the copyright and all other rights are reserved to their respective owners and/or rest with the persons and institutions mentioned. Interesting volumes to try can be found at J3D.org

3-D reconstruction of Brassica Napus organelles. Nucleus (A), 'amyloplasts' (B) and vacuole (C) by Gary Chinga. Scale 10 m. See http://www.ciencia.cl/CienciaAlDia/volumen5/numero1/articulos/articulo4.html.

The above are confocal microscopy images of a cell which has a conjugate of interest which is in the cell stained with Cy-3. Fluorescein is used in the external solution to outline the cell. The two rendering files are depth coded renderings of two such cells (they are live cells).

skull_left.gif (43816 bytes)skull_right.gif (44855 bytes)
Stereo rendering of front of human skull with both orbits (reduced, Visible Human CT 256x256x256). Look right between the two images into infinity and you may see the stereo effect. The orbits are anatomically incorrect, since the bone is very thin in some regions (especially the ethmoid), and cannot be rendered. Gradient determination in these areas needs some work, a good subject for a PhD thesis.

Depth coded rendering of z-series of a HeLa cell, transiently transfected with mitochondrially targeted DsRed1. The z-series was obtained with a Biorad MRC1024 LSCM and deconvoled using a 3D blind deconvolution package from Noran. The rendering was depth coded to demonstrate that there are mitochondria above and below the nucleus rather than in it, as they appear to be in a regular surface rendered image. Image courtesy of  Tony Collins tony.collins@bbsrc.ac.uk .

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Rotating Human brain (MRI, 256x256x182) - The MNI single subject brain. Courtesy of Chris Rorden.

brain_lesion.jpg (9122 bytes)
Brain with lesion in blue (MRI + ROI, 128x128x91). Lesion volume produced by MRIcro, courtesy of Chris Rorden.

Rendering of front and back of z-series of dystrophin distribution in an isolated rat cardiac myocyte. The stain is a rabbit polyclonal antibody to dystrophin, courtesy of Dr. James Ervasti (http://www.physiology.wisc.edu/www/ervasti.html) of the University of Wisconsin, Madison, decorated with an Alexa 568 secondary antibody from Molecular Probes.  Microscope is a Bio-Rad 1024 mixed gas Kr/Ar from the Keck Biological Imaging Lab (http://keck.bioimaging.wisc.edu/). The microscope settings were excitation 568, iris 4.0, gain 1200, blev -5, z-step size 0.5 micron, 100X objective. Rendering courtesy of Seth Robia, who is with the Department of Physiology at the University of Wisconsin. More renderings can be found at his website http://www.physiology.wisc.edu/~robia/.

echiura.gif (32203 bytes)
Nervous system of Echiura, courtesy of Rene Hessling. More information and cine renderings can be found at his fine website.


metaphase2.jpg (35557 bytes)
Mouse embryo metaphase. The chromosomes show quite nicely. The cell is from a two cell stage mouse embryo stained with SYTO-13. The Z-stack was acquired with a Biorad 1024 LSCM. x60 objective, zoom x2. Image 2000 and courtesy Tony Collins  at the Laboratory of Molecular Signaling, The Babraham Institute, Cambridge CB2 4AT, UK.

cinescala.gif (289946 bytes)
Cinescala in grayscale, converted to .GIF animation format (manually) in Microsoft Image Composer.

Tony Collins tony.collins@bbsrc.ac.uk uses VolumeJ to make surface plots. This example shows the elementary calcium events preceding a calcium wave. HeLa cell, loaded with the calcium-sensitive fluorophore, Fluo-3 and imaged whilst responding to application of histamine. All image processing was done with ImageJ. The image stack was converted to 32-bit and divided by the average of the first 5-frames (F/F0). A. Frame taken at the peak of the calcium-release response. (B) The line of pixels along X-Y was taken and stacked side by side from right-to left to generate a "pseudo-line scan". This allows visualisation of the progression of the wave from its initiation site. Calcium concentration is encoded by the intensity of the green pseudo-colour. (C) Surface-plot of B, processed with VolumeJ using depth encoding (see "Surface-plot manual" t.b.a.). Calcium concentration is encoded in the height of the surface-plot. Two elementary calcium events are visible prior to the wave, the second, larger event occurs at the initiation site of the wave. More details regarding elementary-calcium events can be found in Bootman and Berridge 1995 (Cell 83, p675-678) and references therein. Image courtesy Tony.

(c) 1999-2003, Michael Abramoff. Last updated 27-May-04.