7.2  Image Handling - Using Slicer


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   Slicer (an outdated program) can perform such operations with a good degree of control and flexibility on voxels of arbitrary aspect ratio (i.e. not necessarily cubic, e.g. when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  Slicer (due to a bug in the outdated version we have) requires a series of bitmap files to represent the volume image data.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:

command_prompt_on_desktop.gif (1803 bytes)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)

Convert individual tiff files into bitmap files using LViewPro.exe LViewPro Help

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

Start Slicer.exe


Icon_Inverted_Laser.GIF (1500 bytes) Icon_book_white.gif (1143 bytes) 1998-2003 Michael Chua, Cell & Molecular Physiology, UNC.  All rights reserved. 
To Confocal Homepage To Operating the confocal To Booking the confocal Go back a page Comments: Dr. Michael Chua