Editing Comparative genomic hybridization (section)

===Fluorescence visualisation and imaging===
A [[fluorescence microscope]] with the appropriate filters for the [[DAPI]] stain as well as the two fluorophores utilised is required for visualisation, and these filters should also minimise the crosstalk between the fluorophores, such as narrow band pass filters. The microscope must provide uniform illumination without [[Diatonic and chromatic|chromatic]] variation, be appropriately aligned and have a "plan" type of objective which is [[apochromat]]ic and give a magnification of x63 or x100.<ref name="Weiss,Hermsen,Meijer,VanGrieken,Baak,Kuipers,VanDiest" />

The image should be recorded using a camera with spatial resolution at least 0.1&nbsp;μm at the specimen level and give an image of at least 600x600 pixels. The camera must also be able to integrate the image for at least 5 to 10 seconds, with a minimum photometric resolution of 8 bit.<ref name="Weiss,Hermsen,Meijer,VanGrieken,Baak,Kuipers,VanDiest" />

Dedicated CGH software is commercially available for the image processing step, and is required to subtract background noise, remove and segment materials not of chromosomal origin, [[Normalization (statistics)|normalize]]  the fluorescence ratio, carry out interactive karyotyping and chromosome scaling to standard length. A "relative copy number karyotype" which presents chromosomal areas of deletions or amplifications is generated by averaging the ratios of a number of high quality metaphases and plotting them along an ideogram, a diagram identifying chromosomes based on banding patterns. Interpretation of the ratio profiles is conducted either using fixed or statistical thresholds ([[confidence intervals]]). When using confidence intervals, gains or losses are identified when 95% of the fluorescence ratio does not contain 1.0.<ref name="Weiss,Hermsen,Meijer,VanGrieken,Baak,Kuipers,VanDiest" />