Download Using AGScan

Sigenae
February 2006 Edition
General Overview
This chapter presents an overview of the whole process, some information about image file types and
quality and gives the software install procedure.
The process
To start the process you need at least :
• a micro-array image (different formats can be used),
• a grid file (generated in AGScan see next chapter section),
• AGScan installed (see install procedure below)
Notice that AGScan works with 16bits-unsigned grayscale images.
By default, AGScan input image format is the TIFF format but ISAC format (INF/IMG) is also
recognized by a plugin automatically provided into all AGScan versions.
The grid file can be generated with AGScan or provided by someone having generated it. To share a
grid you have to be sure that the micro-array and the definition used to scan the image are the same.
The process can be split in five steps :
- experiment image(s) loading
- grid loading
- global alignment : This step can be done by
AGScan or by the user. It corresponds to the
general alignment of the designed grid on the
image(s).
- local alignment : This step is done by AGScan.
Starting from the global alignment AGScan tries
to figure out what the small local changes are to
fit the sub-grids as well as possible to the image.
- quantification : This step is done by AGScan.
Starting from the local alignment coordinates
AGScan calculates for each spot several
quantification values. These values will be
presented later on.
Image(s)
Grid
Glocal Alignment
Local Alignment
Quantification
As presented before, AGScan is able to process an image and a grid without any human help. This is a
very important and user asked AGScan feature.
AGScan User Manual
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