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Imageconversion configuration

This configuration keyword defines the program which converts the scanned input image into a hidump image file as used by the image interactive editors and their anaylsis programs.

Image and its external analysis modules can only deal with their own image file format, which is the Hidump format. This is a very simple file format, which is quick to load and display once the original image dat has been converted.

Whatever data gathering tool (scanner or ABI machine) you use, it probably won't produce a hidump file of the right dimension and orientation. The program "im3conv" converts the raw DAT, GIF, TIFF and ABI-gel files into hidump images.

The image conversion takes place before Step 1 is started for the first time on a gel. For large images it may therefore take a little while, before you see the gel image.

Command line arguments

The image conversion program is called im3conv. It has two command line aguments :

The rotation gel parameter specifies how to rotate the original raw image to get to the converted image which has horizontal lanes (The scanner may produce an image with a different orientation).

The raw-imagefile is the file name of the image that was written by the scanner or ABI-machine. The imimport script should have placed that file in a gel diretory and called it image.<format>. The format is determined from the default parameter "image file format" as configured in the project defaults dialog.

The configured command line for $imageconversion is :

im3conv -R$rotation $raw-imagefile

It may be useful to include the complete directory path to the im3conv executable to resolve ambiguities caused by different $PATH values in the shell-setup for different users.

Last modified : November 1999 Image 3.10

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