efg's Research Notes

 


ZeissToSGI (Zeiss AxioVision to SGI SoftWoRx) TIFF Conversion Utility (Version 1.1)
 

Earl F Glynn
Stowers Institute for Medical Research
8 October 2002

 


Download (available under GNU General Public License):   
Windows Executable
  |  Delphi Source Code
(with TiffTags utility)

 

Sample TIFFs For Conversion 

 

Also see:  TiffTags Utility


Purpose
The ZeissToSGI utility program converts from a Zeiss AxioVision TIFF file to one that can be read by the SoftWoRx software on SGI boxes.

Background
While Tagged Image File Format (TIFF) images are common, there can be many problems using TIFF files, especially created on a variety of scientific devices. These TIFF problems resulted in some suggesting in jest that TIFF really stands for "Thousands of Incompatible File Formats."

The TIFF specification is very broad and flexible, but many software vendors do not need and do not implement all possible "tags" allowed by the specification. In this case, TIFF files created by Zeiss use a separate "strip" for each row in the image, but SGI's software expects input TIFF files to have the whole image stored as a single strip.  There is also a difference in how "16 bit" data are stored within a 2-byte word of storage.

Zeiss likely was providing a flexible framework to store quite large images and only read the part that was needed.  SGI, on the other hand, was expecting to process an image that could be held in memory, and didn't care about reading such large images.

See additional TIFF information with the TiffTags utility.

Software Requirements
Tested only using Windows 2000, but should work on other versions of Windows.

Download the executable and test images to any convenient directory.  No special installation is required.

Step-by-Step Procedure
1.  Click on the ZeissToSGI.EXE to start the program.

2.  Press the Load button to select one or more files:  In the Open Dialog, select a single file by clicking on the file name and pressing the Open button.

Select a group of files in any of several "standard" Windows ways. (1) Select the first file by clicking on it. Select additional files by using Ctrl-Click. (2) Click and drag to "lasso" a group of files with the selection box, as shown below:

 

In the dialog box above, the images with a prefix of "Axio" can be converted by this program, but the "Final" image cannot, since it is not in a Zeiss format.

 

The selected image (or the last one if more than one is selected) is displayed:.

 

Note the message at the bottom left of the displayed image:

 

Only "Likely Zeiss" files will be converted.

 

3. Press the Convert button to display the selected image(s) one at a time, and to convert each from one TIFF format to the other TIFF. Each new file is given the original name with a "_SGI" suffix". The memo box at the bottom of the screen gives feedback about the conversion process.

 

 

Note above that file 3 was converted, but files 4-9 were ignored since they were not in the "Likely Zeiss" format.

 

If a file of a given name already exists, the following message is displayed:

 

Press the Yes button to overwrite the file.

 

The finale message "Conversion Completed" appears after all files have been converted. If desired, press the Cancel button to terminate the conversion process.

 

 

Discussion

 

Summary of Differences between Zeiss Axiovision TIFF and SGI SoftWoRx TIFF

 

Type Zeiss Axiovision SGI SoftWoRx
BitsPerPixel full 16 bits 16 bit word with 12 bit data
TIFF "Strips" Multiple strips.  Selected parts of image can be loaded. Single Strip for whole image.
Endian Little Endian (only?) Little or Big Endian (?)
Displays in Photoshop? Yes, quite well Very dark, nearly black image but looks OK after autocontrast:  Image | Adjust | AutoContrast
How detected? StripsPerImage > 1  AND BitsPerSample = 16 AND
SamplesPerPixel = 1
StripsPerImage = 1 AND BitsPerSample = 16 AND
SamplesPerPixel = 1
Pixel modification in utility program to auto-display image with reasonable contrast Shift 16-bit word 8 bits to right to give 8-bit grayscale pixel.
xxxx xxxx yyyy yyyy ®
0000 0000 xxxx xxxx

Shift 16-bit word with 12 bit data 4 bits to right to give 8-bit grayscale pixel

0000 xxxx xxxx yyyy ®
0000 0000 xxxx xxxx

 

 

The Aldus TIFF Spec (TIFF Revision 6.0, June 3, 1992) apparently only specifies 4- or 8-bit grayscale images and does not specify what "standard" should be applied to 12-bit or 16-bit data.


The TiffTags.Exe program can be used to view "tags" in a TIFF file, and for some selected types of TIFF, the image can also be optionally displayed on the Image tabsheet.

 

A Zeiss file, which can be converted by the ZeissToSGI program, will look like this in TiffTags:

 

 

Once converted by ZeissToSGI, the TIFF tags will appear like this:

 

 

 

Acknowledgement:  Test images are courtesy of Ting Xie.

 


Updated
30 June 2005