8.1  Image Handling - Using Confocal Assistant 4.02 with Leica z-series or t-series Tiff image files


Confocal Assistant 4.02 (CAS) is an excellent image stack (e.g. serial sections (z-series) or time lapse (t-series)) viewing and processing program for Windows 3.1, which was created and copyrighted by Todd Clark Brelje.  It performs functions such contrast enhancement consistently on each image of whole stacks, simple maximum brightness projections of z-series stacks as well as generating stereo and anaglyph pairs.  Confocal Assistant is intended for use with Biorad confocal PIC format image z-series stacks, and has limited file conversion capabilities.  PIC file stacks of multiple channels may be merged together into and red/green/blue AVI format movie, which is viewable in windows.  Despite its limitations this program is useful and quick enough, that it is well worth the effort of converting Leica Tiff z-series stacks or time series into Biorad PIC format, and if desired from PIC format back into a series of bitmaps.  This program is free for academic use.

Confocal Assistant (CAS) can only be run in Windows and does not handle long files names. i.e. file names should be 8.3 (name + extension) otherwise a short, and sometimes garbled, name is generated from the long file name.  To view an image captured as a Leica format TIFF file one needs to first convert it into a bitmap series using tiffsplit4.exe, then convert the bitmap series into a PIC format image file using bmp2pic.exe.  The resulting PIC format file contains an image series, which can be opened by CAS.


To be able to use Confocal Assistant 4.02 to view Leica Confocal Tiff format z-series or t-series (time lapse), two image file conversion programs need to downloaded and installed along wih CAS.  The file conversion programs, Tiffsplit4.exe and bmp2pic.exe are DOS32 command line programs and need to be placed, for example, in the C:\WINDOWS\COMMAND directory, in order to runable from the command prompt of your computer.  Tiffsplit4.exe and bmp2pic.exe can then be run inside a DOS box (Command Prompt in Windows 9X, NT or 2000).  CAS402 is an install program and needs to downloaded into a temporary directory and executed.  The CAS402 install program will install the program in a directory of your choice, and create an entry in the start menu of Windows.

The Details:

Go To 8.2   Converting Leica Tiff image format into Biorad PIC Image format for use with Confocal Assistant

Go To 8.3   Viewing a z-series animation with Confocal Assistant or making a maximum brightness projection, etc. 

The Down Side:

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Last updated 05-06-2002

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