Brief Overview:

3D rendering of a series of serial optical sections, volume image, involves mathematically reconstructing a view through the volume image from an arbitrary view point with chosen lighting conditions.  A common and robust rendering method uses the transparency model, where each, sample in the column, voxel element, is assumed to have a certain brightness and transparency.  For fluorescence data each voxel is assumed to be self emitting and to have a transparency factor either proportional to the intensity of light emitted (surface like view) or have a fixed low transparency value (jello view).   Slicer (an outdated program) can perform such operations with a good degree of control and flexibility on voxels of arbitrary aspect ratio (i.e. not necessarily cubic, e.g. when z-thickness is several time greater than x-y size as is typical of volume data acquired on a confocal microscope).  Slicer (due to a bug in the outdated version we have) requires a series of bitmap files to represent the volume image data.

The Details:

Convert multipaged tiff image file into individual tiff files.

e.g. Open a DOS box (command prompt) and select the desired drive letter (e.g. e: enter) and change to the desired path (e.g. cd  \users2\fred enter)

• e:\users2\fred>   tiffsplit    sim.tif   enter
• e:\users2\fred>   tiffsplit    sim.tif   -g   enter  (-g converts images into grayscale)

Convert individual tiff files into bitmap files using LViewPro.exe

e.g. make sim01.bmp, sim02.bmp ... to sim20.bmp from sim01.tif, sim02.tif ... to sim20.tif

• File -> Multiple Open
• In "List files of type" select "TIFF (*.tif)"
• just below in "Open destination" choose "Batch conversion" 
• press the "setup" button and choose "windows BMP"
• browse to directory containing tiff files and select the desired files with the mouse
• press "Add->" and then "OK" and "Yes" to "Are you sure you want to drop to Batch conversion?"
• A bitmap file series will be created.  e.g. sim01.bmp to sim20.bmp

Start Slicer.exe

• Import bitmaps file series
• Set aspect ratio of voxel by choosing z-axis scale
• Selected a look up table scheme
• Set transparency in look up table
• Choose view angle in 3D space
• Hit render
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• Don't know what to do?  Get help!!!

					© 1998-2003 Michael Chua, Cell & Molecular Physiology, UNC.  All rights reserved.
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