Patent Application
20060213994
NOT APPLICABLE
The present invention relates generally to a scanning mechanism and, more specifically, to a barcode reading mechanism for a DNA Microarray Scanner that identifies and quantifies genetic material.
A microarray scanner includes a carousel that has radial slots. The carousel is rotatably mounted on a support that includes an annular wall surrounding the carousel. The annular wall has an access opening to the carousel. Each radial slot is adapted to receive a holder containing a transparent slide, e.g. a 1″ by 3″ glass slide. Each slide is located in a custom slide holder. A biological sample to be examined is located on one side of the slide. The sample is DNA or RNA material extracted from a biological sample. In a process known as Hybridization, the sample is allowed to bond with known DNA sequences or probes deposited in a two-dimensional array on the glass slide. A barcode that identifies the specimen to be examined is located on one side of the slide and spaced from the sample. The barcode is used to identify the sample on the slide in all phases of its processing, including hybridization, scanning and software analysis. A slide examination or scanning station is located outside of the carousel. An instrument at the slide examination station scans and produces a high-resolution image file of the array. A barcode reading mechanism is located between the examination station and the carousel just outside the access opening.
During operation of the scanner, the carousel is selectively rotated so as to position a selected holder and contained slide at the access opening. A transfer mechanism grasps the selected holder and carries it through the barcode reading station to the slide examination station. The transfer mechanism is a robotic arm-like assembly used to transport the slide holder and slide out of the carousel before scanning, and back into the carousel after scanning. As the holder and the slide move through the barcode reading station, the barcode reader reads the barcode on the slide. The barcode on the slide is in the form of a label or strip that is applied to one of the surfaces of the slide. In the past, biological scanning mechanisms were set up so that a probe array containing a biological specimen was located on one side of the slide and a conventional barcode label or strip was located on the opposite side of the slide. A conventional barcode label or strip has black spaced bars on a white reflective background. The barcode label was read by a barcode reader located at the barcode reading station on the side of the station facing the side of the slide containing the barcode.
For many sample scanning procedures, the barcode is required to be placed on the same side of the glass slide as the biological specimen sample or the “array” side of the slide. Since the barcode reader is located on the opposite side of the “array” side of the slide, a conventional barcode label cannot be read. In order to accommodate the above-described sample scanning procedures, a translucent barcode label was used. The translucent barcode label has black bars on a translucent background. An incident light beam from the barcode reader is projected through the transparent slide to the barcode label. A portion of the light beam is returned back toward the barcode reader to enable the barcode to be read by the barcode reader. Light from the barcode reader can be infrared, laser, or any state of the art light source. Since the background of the barcode label is translucent, a portion of the incident light beam passes through the barcode label so that the portion of the light beam returned back to the barcode reader is not as strong as the incident light beam. Normally, a series of incident light beams are directed toward the barcode as the slide passes through the barcode reading station to obtain several identifying signals for averaging to provide a consensus signal. In many cases the signals are not strong enough to provide an accurate identification of the barcode being read. This problem becomes more acute if there is any degradation of the label during treatment of the slide during the steps in pre and post hybridization operation, i.e. washings.
The translucent barcode label must also be used in a microarray scanning mechanism in which the barcode reader is located on the “array” side of the slide but the barcode label is required to be placed on the opposite side of the slide. For example, the barcode label might need to be changed and applying it on the non-array side of the slide minimizes any contact with the array. Having the barcode label on the non-array side of the slide also minimizes any contact with wash chemicals during array processing.
What is generally needed is a barcode reading apparatus that is able to read translucent barcode labels with high accuracy.
In one aspect, the present invention provides a barcode reading apparatus for reading a translucent barcode label that has opaque indicia such as spaced black bars on a translucent background. The barcode reading apparatus includes a transmitter for projecting an incident light beam toward the label so that some of the light is returned back from the translucent background toward a detector portion of a barcode reader and some of the light passes through the translucent background to a light returning device on the opposite side of the slide, said light returning device bearing a light returning surface. The term “light returning device” is used herein to describe a device bearing a light returning surface. A light returning surface is a surface that is capable of receiving a beam of light from a source, and, in reaction to receiving the beam of light, radiates a return beam of light toward a light sensor associated with the source. The portion of the incident light beam that strikes the light returning surface is returned back through the slide toward the detector portion of the barcode reader. This portion of returned light produces a signal that is added to the signal produced by the portion of the incident light beam initially returned from the translucent background of the barcode label to produce a much stronger identifying signal.
The invention is described in the accompanying drawings in which:
Referring to
Referring to
Referring now to
Referring particularly to
During operation of the scanning mechanism 10, the slide tray 18 is rotated until a selected holder and slide to be scanned and analyzed is aligned with the opening 22. The selected holder 26a containing the selected slide is grasped by a transfer mechanism, not shown, and removed from its respective slot 25. Slide holder 26a is transported through the barcode reading station, generally indicated by the reference numeral 50, to the specimen scanning apparatus, not shown.
Referring to
As the holder 26a and slide 28a pass through the barcode reading station 50, between light returning device 36 and the barcode reader 30 as shown in
A performance feature of a barcode reader is its Print Contrast Signal. Print Contrast Signal=(Reflectance of Space−Reflectance of bar)/Reflectance of Space. Reflectance is used herein to describe light returning capacity by any mechanism, not just by formal reflection. The term “space” refers to the space between the bars in the bar code. Print Contrast Signal measures the contrast between light returned from the bars and light returned by the spaces on the barcode label. The following is a comparison of readings of a translucent barcode with and without a light returning device such as light returning device 36.
Without Light Returning Device
Reflectance of Space=R1
With Light Returning Device
Reflectance of Space=R1+T2
Now T2>0. Therefore it follows that:
Reflectance of Space with Light returning device>Reflectance of Space without Light returning device
Since the Reflectance of the bar is unchanged, it follows that:
Without Light Returning Device
Print Contrast Signal=1−Reflectance of Bar/Reflectance of Space=1−Reflectance of Bar/R1
With Light Returning Device
Print Contrast Signal=−Reflectance of Bar/(R1+T2)
Since,
(R1+T2)/Reflectance of Bar>R1/Reflectance of Bar, it follows that their negative reciprocals are related as,
−Reflectance of Bar/(R1+T2)>−Reflectance of Bar/R1 and,
1−Reflectance of Bar/(R1+T2)>1−Reflectance of Bar/R1
Therefore, Print Contrast Signal (with light returning device)>Print Contrast Signal (without Light returning device). This assumes that the reflectance (light returning efficiency) of the light returning device is 100%. However, it can be shown that any significant amount of return light from the light returning device improves the Print Contrast Signal.
The present invention enables the translucent barcode label on the glass slide to be read by the barcode reader 3 with high efficiency. Barcode labels with barcodes printed on opaque white background or transparent background can also be used with the barcode reading apparatus of the present invention.
Some styles of barcodes with imperfections in their printing can also be read. For instance:
By enabling the reading of transparent and translucent barcodes, the invention allows these styles of barcodes to be placed on either the front or the back surface of the slide. Prior to the present invention the barcode reader was required to have a fixed orientation relative to the slide, namely that it be positioned facing the front side of the glass. Physical space availability or accessibility restrictions might make this requirement difficult to implement in some processes. No such restrictions are needed when transparent or translucent barcodes are read by the barcode reading apparatus of the present invention.
