Genome Technology Center

Scanner

Scanner This instrument was developed in Pat Brown's lab in the Biochemistry Department

We have constructed a two-color (green and red) laser-fluorescence-based scanner for scanning a medium-density array of cDNA probes hybridized onto coated glass slides. A typical slide contains upto 10000 probes, arrayed in a 1 sq. inch area. Two-color laser scanning allows quantitative studies of gene-expression in two samples simultaneously. The two samples are distinguished thru labeling with the fluorescent dyes Cy3 and Cy5.

The fluorescence signal is amplified by PMTs and collected by a fast A/D board. A typical scan takes about 15 minutes and collects about 14 million pixels of 16-bit data for each channel. The software driving the xy-scan motion control and the data acquisition board is written in Labview by National Instruments Corp.. After data averaging and compression, the data files for each channel are about 1 Mbyte large, at the 16-bit resolution. The data files are compatible with and are readily analysed by AIS imaging software as well as NIH Image. A dynamic range of 1000:1 is easily obtained. This value is limited by background 'biochemical' noise, inherent in the present protocol for slide preparation. 

The resolution of the scan in the present system is limited by the laser spot size and is approximately 10-20 microns. The motion control system has a specified resolution of about 3 microns. Thus, features on the order of 100 microns are easily resolved by the scanner. 

Drawings for this instrument are available from Pat Brown's lab

Scanner
Scanner Image
Green Laser
Green Laser
Red Laser
Red Laser
Slide Being Scanned
Scanning Slide - #1
Scanning Slide - #2
Scanning Slide - #3
Scanning Slide - #4
Scanning Movie
Combining 2 Lasers
Combining 2 Lasers
Lasers Movie
Optical/Motion Control System
Optical/Motion Control System
Close-up of Control System
Close-up of Control System
Laser Entering Control System
Laser Entering Control System

Stanford Medicine Resources:

Footer Links: