The image to be analyzed is called the primary image. It consists of two files: the image data file and the ascii import file. The import file, which includes a string specifying the data file, is the one selected by the user. Also selected for input to analysis are a gel-format file and a template-definition file. The gel-format file is an ascii file listing the lane labels associated with the image. The template-definition file describes a template of size-standard bands, listing mobility and base-pair size for each band; the input image is warped against this template to output a spatially-normalized primary image. The normalized image is of the import variety, with its own ascii import file and image data file. Experimental bands are then detected in the non-size-standard lanes of the normalized image; mobilities and sizes of these bands can be saved in the import file of the normalized image. As an option, individual lane images can be saved before and/or after normalization. Table 2.1 lists the various steps of analysis to show which files are input when, which are output, and which are updated.
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Analysis Step Input File Output File
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Load Raw Image Import
Raw Image Data
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Enter Image Information Gel-Format
Template-Definition
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Crop Image
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Detect Lane Boundaries
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Detect Size-Standard Bands
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Save Results Import#
Lane Images*
Lane Profiles*
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Normalize Raw Image Normalized Import
Normalized Image Data
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Detect Experimental Bands
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Save Results Normalized Import#
Normalized Lane Images*
Normalized Lane Profiles*
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# Update existing file.
* Option; by default, these are not saved.
Forward to Chapter 2, Section 2.9