WO2010081536A1

WO2010081536A1 - A biochip reader for qualitative and quantitative analysis of images, in particular for the analysis of single or multiple biochips

Info

Publication number: WO2010081536A1
Application number: PCT/EP2009/050304
Authority: WO
Inventors: Antonella De Montis; Cassandra Lauterio; Lucio Deiana; Simone Musiu; Stefania Lostia; Francesca Perseu; Michele Desogus; Sinibaldo Perseu
Original assignee: Bcs Biotech S.P.A.
Priority date: 2009-01-13
Filing date: 2009-01-13
Publication date: 2010-07-22

Abstract

A biochip reader for qualitative and quantitative analysis of images, in particular for the analysis of single or multiple biochips with different colorimetric signals for different targets of biological interest such as drugs or nucleic acids, fat acids and proteins from viruses, prokaryotes and eukaryotes organisms, obtained from human, animal, vegetal or environmental biological samples. Said biochip reader comprises: - an optical head 18, able to moving itself in one direction Y, comprising: - at least one visible light source 20 or 21 - at least two CCD sensors 16 and 17, attached each other; each CCD comprising a reflective lens set 24 and a focalising lens 25; - control means, able to control said optical head 18 and its one-dimensional motion. Being each CCDs attached each other, then each half, or portion of, image has an identical position or angle error of the other half, or portion of, image, so as the joining process becomes immediate.

Description

A BIOCHIP READER FOR QUALITATIVE AND QUANTITATIVE ANALYSIS OF IMAGES, IN PARTICULAR FOR THE ANALYSIS OF SINGLE OR MULTIPLE BIOCHIPS Field of invention The invention relates to a biochip reader for qualitative and quantitative analysis of images, in particular for the analysis of single or multiple biochips with different colorimetric signals for different targets of biological interest such as drugs or nucleic acids, fat acids and proteins from viruses, prokaryotes and eukaryotes organisms, obtained from human, animal, vegetal or environmental biological samples.

State of the art

It is known an automatic apparatus for qualitative and quantitative analysis of mono and polychromatic images from miniaturized supports for macro and microarrays, well known as biochip, either in single or multiple format or realised as glass slides or microplates of up to 384 wells. The support surfaces can be shaped with natural reflective materials or made of glass, organic polymers as acrylic resins, polypropylene, polystyrene, polyethylene, polyvinyl chloride, polysulfone, polycarbonate, cellulose acetate, rubber, latex, polyethylene terephthalate, acrylonitrile-butadiene-styrene (ABS), acrylonitrile-styrene or their combinations.

Biomolecules are fixed on the support and detectable by colorimetric techniques like E. L.I. S. A. (Enzyme-Linked Immunosorbent Assay).

The support dimensions are standardized, so the biggest number of signals acquirable by the system is between 25 dots, for biochip of a single well in a microplate of 384 wells, and 100 dots, for biochip of a single well in a microplate of 96 wells, up to a maximum of 20.000 signals for supports like glass slides. The kind of molecules that can be fixed on these biochips and then studied by common and cheap colorimetric techniques, is wide: oligonucleotide probes for detection of complementary nucleic acids, such as specific amplicons from viruses, bacteria, parasites, OGM but also fat acids, proteins, drugs, toxins of various chemical nature, that could be searched directly or indirectly, for diagnostic or environmental monitoring purposes. The known automatic apparatuses are able to acquire and analyse only signals produced by fluorescence or chemiluminescence. In fact, the technology of acquisition and analysis of images produced by colorimetric reaction on the biochip, although less expensive, presents many drawbacks. In order to solve such problems it was suggested a colorimetric biochip reader having an optical module with a visible light source, three mirrors, that focalise an image through a lens on a single CCD (Charge Coupled Device) sensor. This module first moves in a first direction towards a first position by acquiring an image of a few wells; then it moves along the right-angled axes, finally it moves towards a second position and proceeds to acquire the image of another portion of microplate. All such images, joined together by a software, are then analysed and compared with pre-defined patterns.

Therefore, said optical module moves along a 2-dimensional space scanning one raw of wells at a time, and only 4 wells per raw. The main drawback of said optical module is that the motion sequence depends on the width and positioning of each raw of well.

Consequently if a microplate includes larger o smaller wells, the optical module has to change the width of its motion and discard a region of image falling out of a raw of wells at a time, otherwise it should have a position error in the motion control lower than the optical resolution so as could be possible to join two or more images as a mosaic also when the boundary line falls on a well. Moreover, if a microplate comprises smaller wells, the CCD scans more then one raw of wells at a time. Therefore, if the width of such wells placed side by side is larger or smaller then the length of the CCD, then, when all images have to be joined, many regions have to be superimposed each other by wasting time and a portion of the CCD capability.

Such drawbacks impose constraints in terms of well width and also in terms of scanning resolution, so as it follows that it is impossible to go beyond the limit of 25 signals per well. Obviously, another drawback of said apparatus is the acquisition dynamics, which requires long waiting times necessary for all the movements. Summary of the invention

The purposes of the present invention is to overcome said above described drawbacks and provide a fast and efficient biochip reader, able to scan an entire microplate by a single pass. An object of the present invention is a biochip reader for qualitative and quantitative analysis of images, which according to claim 1 , comprises

- an optical head, able to move in one direction, comprising:

- at least one visible light source and

- at least two CCD sensors, attached to each other; each CCD comprising a reflective and focalising lens set;

- control means, able to control said optical head and its one-dimensional motion. Advantageously, as the CCDs are attached to each other, then each half, or portion of, image has an identical position or angle error as the other half, or portion of, image, so as the joining process becomes immediate, because there is no positioning error between two adjacent images. Therefore, the optical module motion is independent of the well width and limited only by the size of a container containing the microplate to be scanned.

Dependent claims define preferred embodiments of the invention.

Brief description of the drawings The purposes and advantages of this invention will become clear from the following detailed description of a preferred embodiment and of its variants and from the drawings that are attached hereto, which are merely illustrative and not limitative, in which: figure 1 shows a biochip reader according to the present invention; figure 2 shows the biochip reader in figure 1 with its container in transparency; figures 3 and 4 shows the biochip reader in figure 2 during a scanning operation; figure 5 shows an exploded figure of the biochip reader in figure 1 with cover removed; figure 6 shows the biochip reader in figure 1 with cover removed; figure 7 shows an upper view of the biochip reader in figure 6; figure 8 shows a longitudinal section view of a portion of the biochip reader in figure 7; figure 9 shows a transversal section view of a portion of the biochip reader in figure 7; figure 10 shows a lower side view of the biochip reader.

The reference letters and numbers identify, in the figures, the corresponding elements and components

Detailed description of the invention

In a preferred embodiment the biochip reader is able to scan an entire microplate in a single scanning process along the Y axis by means of an optical head 18 comprising: - two linear CCDs 16 and 17 lined up and consecutively attached each other along the X-axis, each comprising a dichroic and reflective lenses set, positioned inside the optical head (shown in Fig.5);

- two Cold Cathode Fluorescence Lamps CCFLs 20 and 21 , shown in figure 10, parallel to each other along an X axis, perpendicular to such Y axis, able to light up at least a well, and positioned under the optical head at a minimum distance, for example of 3 mm, between each other, both preceding the two CCDs 16 and

17.

The first CCD sensor 16 has a first optical aperture 23, and the second CCD sensor 17 has a second optical aperture 22, adjacent to that first optical aperture. As shown in figure 9, a scanning process allows to scan simultaneously 8 biochips, 4 for each CCD sensor, so that when a microplate comprises 8 x 12 wells, it can scan a total number of 96 biochips in only one scanning pass.

Advantageously, each well is lighted up in the same right way. So as the error probability in a pattern comparison becomes isolated. The biochip reader, according to figure 5, comprises a container 1 , inside of which is placed the optical head 18 that, by means of a transmission system 10 and 1 1 , is moved forth and back along the Y axis. Said transmission means comprise two sliding track lines 1 1 and 1 1 ', parallel to Y axis, over which the optical head is able to slide, and a dented belt 10 dragged by a first motorized dented gear 3 rotatably associated with the container 1 ; said dented belt being connected to the optical head 18. A first electric motor 5 associated with such first motorized dented gear

3, is shown in figure 10. The carrier 4 has, on the bottom, a built in dented transmission bar 12, able to engage with a second motorized dented gear 7, comprising a second electric motor 9, rotatably associated with the container 1 , to allow the movement of the carrier forth and back for the opening and closing, as shown in Fig. 5 and 10. In this preferred embodiment the carrier opening is according to the Y-axis.

On top of the carrier it is possible to place an engaging support 8, for example, for microplate 6, comprising a plurality of wells 19, in order to obtain a stable single structure, as shown in figures 5 and 6. On top of said microplate 6 are placed, for example, 96 biochips in as many wells. In figure 8, a longitudinal view of the optical head 18, shows the reflective 24 and focalising 25 lenses set, associated with each CCD sensor 16 or 17. The scanning process starts by placing a microplate 8 on the top 13 of the carrier 4 (see the sequence in figures 1 - 4). The carrier conducts the microplate inside the container by blocking it, so as the optical head 18, moving along the Y axis, acquires the two reflected images.

These two images are transmitted to a computer, through a USB 2.0 port. A software analyses the acquired image comparing it to pre-defined qualitative and/or quantitative patterns (Example: HPV Biochip, figures 1 OA and 10B). By using two or more binding CCDs aligned along the X axes, it is possible to acquire sharp images, instead, using only one wide CCD the image appears deformed at both edges aligned along the Y axes.

Each CCD has a resolution of 1200DPI 16-bit or higher that allows the analysis of a bigger number or of smaller quantities of targets detectable by colorimetric techniques and therefore increases the ability of the instrument to process up to 384 biochips.

Only two independent images obtained by the optical head 18 moving along only one axis, allows to save time during the scanning process and during the joining process.

So as, the biochip reader allows the simultaneous detection and analysis of colorimetric mono and polychromatic signals from single or multiple biochips for targets of biological interest such as: drugs or nucleic acids, fat acids and proteins from viruses, prokaryote and eukaryote organisms, obtained from human, animal, vegetal or environmental biological samples.

It will be apparent to the person skilled in the art that other alternative and equivalent embodiments of the invention can be conceived and reduced to practice without departing from the scope of the present invention.

It will be possible for the person skilled in the art to embody the invention without introducing any further construction details.

Claims

1. A biochip reader for qualitative and quantitative analysis of images, in particular for the analysis of single or multiple biochips comprising

- an optical head (18), able to move in one direction Y, comprising: - at least one visible light source (20 or 21 )

- at least two CCD sensors (16 and 17), attached to each other; each CCD comprising a reflective (24) and focalising lens set (25);

- control means, able to control said optical head (18) and its one-dimensional motion.

2. Biochip reader as in claim 1 , wherein each CCD sensor is a linear CCD sensor.

3. Biochip reader as in any of the previous claims, wherein said visible light source comprises two visible Cold Cathode Fluorescence Lamps (CCFLs) (20 and 21 ), parallel to each other along an X axis, perpendicular to said Y direction, able to light up at least a well framed by CCD sensors.

4. Biochip reader as in any of the previous claims, wherein said linear CCD sensors are consecutive and aligned along the X-axis.

5. Biochip reader as in claim 4, wherein said two visible Cold Cathode Fluorescence Lamps (CCFLs) (20 and 21 ) are positioned under the optical head at a minimum distance between each other, both preceding the two CCDs 16 and 17.

6. Biochip reader as in any of the previous claims, further comprising a container (1 ), containing said optical head (18), said control means, and transmission means; said transmission means comprising two sliding track lines (1 1 and 11 '), parallel to said Y direction, over which the optical head (18) is able to slide, and a dented belt (10), connected with the optical head (18), dragged by a first motorized dented gear (3) rotatably associated with the container (1 ).

7. Biochip reader as in claim 6, wherein said container (1 ) comprises a carrier (4) with a built in dented transmission bar (12), able to engage with a second motorized dented gear (7) and rotatably associated with the container (1 ) so as to allow the opening and the closing of the carrier.