WO2002053013A2

WO2002053013A2 - An intellectual bio-chip reader for abundant diagnosis by using an optical identification code

Info

Publication number: WO2002053013A2
Application number: PCT/KR2000/001553
Authority: WO
Inventors: Heui-Jae Pahk; Young-Min Hwang
Original assignee: Diachip Limited
Priority date: 2000-12-29
Filing date: 2000-12-29
Publication date: 2002-07-11
Also published as: WO2002053013A3; AU2001225564A1

Abstract

The present invention relates to a bio-chip reader for abundant diagnosis, more concretely relates to a bio-chip reader by having an optical sensor for abundant diagnosis on medical testing samples on a bio-chip for a short time. The bio-chip reader recognizes an optical identification code on the bio-chip by using its optical sensor. Then, it retrieves patient-related information and bio-chip's information from a database corresponding to the optical identification code and automatically diagnoses the medical testing samples. The bio-chip's information includes at least one selected from the group consisting of sample types of spots, sequences and arrangements of spot-arrays, standard positions and sizes and spaces of spots. Additionally, the bio-chip reader recognizes standard spots sticking on the bio-chip by using its optical sensor. Then, it automatically aligns and classifies spot-arrays sticking on the bio-chip and diagnoses the medical testing samples by using the standard spots.

Description

AN INTELLECTUAL BIO-CHIP READER FOR ABUNDANT

DIAGNOSIS BY USING AN OPTICAL IDENTIFICATION CODE

TECHNICAL FIELD

The present invention relates to a biochip reader for abundant diagnosis, and more

concretely relates to a biochip reader by having an optical sensor for multiple diagnoses on

medical testing samples on a biochip for a short time.

Also, the present invention relates to a high-precision, highly efficient, biochip

arrayer having many potential applications that can recognize an optical identification code

or a reference spot adhered to a biochip using an optical sensor to automatically provide a

diagnosis by abstracting the biochip information, comprised of the content type of the

biochip spot, the sequence and array of the spot array, reference location, size and interval,

and patient information (from the database) corresponding to the specific, recognized

optical identification code.

BACKGROUND ART

A biological chip or biochip is also referred to as a biological array. A biochip has

a substrate including biological material such as nucleic acids. The deoxyribonucleic acid

(DNA) chip is widely recognized and has DNA fixed to its substrate. Another form of

biochip is the protein chip that has proteins fixed to its substrate. The function of biochips is based on the interaction between a target molecule and

a molecule fixed to the substrate. For example, the DNA chip emphasizes the

complementary combination of the oligonucleotides fixed to the substrate and the bases of

the DNA that exist in a sample. The protein chip emphasizes the interaction between

protein molecules such as the antigen-antibody bond or the ligand-accepter combination.

As a result of improved DNA sequencing technology, the gene arrangements of

various living things from bacteria to humans being revealed and much is being learned

about the configuration and the function of the genome due to the accomplishments of

human genome project. However, it is difficult to research the hundreds of pieces of new

gene information discovered daily by using conventional methods because they require

much time and great effort. In order to efficiently research genes, DNA chips are

developed by combining conventional biological technology and mechanical automation

with electronic control technology. The DNA chip means a chip having a substrate on

which a number of DNA are accumulated at high densities and used for retrieving the gene.

Conventional biological research techniques are only capable of studying a small

number of samples; for example, Southern blot, Northern blot, mutation retrieval and DNA

sequencing. However, larger numbers of genes can be more efficiently and automatically

analyzed using the DNA chip.

The DNA chip has many advantages. For example, large quantities of data can be

obtained from one experiment, manipulation of the DNA chip is not difficult and the mechanical automation can be easily accomplished, so research using the DNA chip may

replace conventional biological researching methods. Also, the DNA chip can be widely

applied to various fields such as analyzing the function of the gene, identifying genes that

cause diseases like cancer, gene therapy, issues surrounding the quarantining of animals

and plants, the testing of the food, the development of new medicines, arresting the

mutation of genes, the analysis of how bases are arranged, the testing of tissues, identifying

microorganisms causing disease, and forensic medicine, etc.

The DNA chip is divided into four types according to the manufacturing method

used to produce it. That is, when using the method of fixing oligonucleotides to the

substrate, the DNA chips are sorted into 1) the DNA chip having a pin microarray type,

wherein DNA is always implanted at the same position using a pin, 2) the DNA chip

having an ink jet type, wherein the gene is contained in a cartridge and injected onto a

substrate by electrical force, 3) the DNA chip having a photolithography type, wherein the

DNA is directly multiplied on a substrate using photosensitive chemicals, and 4) the DNA

chip having an electronic array type, wherein those DNA with a minus (-) charge are fixed

at a predetermined position of a substrate and the material with a positive (+) charge is

coated.

Also, a fluorescent reader and an electric signal reader are developed as the

apparatus used to collect data using the DNA chip.

As described above, though many technologies concerning the DNA chip have been developed for use in gene research, technologies needed for using the DNA chip as a

component of an automated disease diagnosis system have not yet been sufficiently

developed.

The immunity diagnosis method of identifying disease has used the blood

corpuscle coagulation reagent, the chemical luminescence immunity measurement method,

the radioactive rays immunity measurement method, and the enzyme immunity

measurement method. According to conventional diagnosis methods, after an antigen is

fixed and has reacted with an antibody in a sample (mainly, serum) obtained from an

organism, the antigen-antibody reaction is measured using a secondary antigen composed

of a radioactive indicator, an enzyme and a fluorescent material. The conventional method,

however, measures far fewer samples than the gene analysis method. Hence, it is difficult

to simultaneously diagnose various diseases, diagnose many persons, or diagnose various

diseases in many persons. Also, conventional methods demand great effort, much cost, and

long periods of time since the analysis procedures thereof are not automated.

The protein chip includes protein fixed to the substrate while the DNA chip

includes DNA fixed to the substrate. Also, the bound reaction of the protein chip demands

multiple reactions composed of the reaction between an antigen and a primary antibody,

and the reaction between the primary antibody and a secondary antibody. In addition, the

separation/combination of the protein chip, and the movement of the protein chip can occur

because each reaction takes place in a chemical reactor. In general, it is understood that antigen proteins or peptides have various electrical

properties (according to the types and the configurations thereof) that are larger than that of

DNA spots. DNA has a negative charge and a DNA spot has a size of 15 to 25 bases up to

approximately 500bp. Also, the protein must be fixed to the substrate while maintaining its

structure because the antigen should not be deformed. Considering such problems, the

method for fixing a protein to the substrate is different from that of fixing DNA, so it is

necessary that each antigen protein be fixed in the optimum range under fixing conditions

optimized to facilitate continuous production. During the detecting procedure, it is possible

to fix various antigen proteins to the same substrate, but all of the DNA's components must

be fixed to a different substrate.

A conventional method of diagnosing using the biochip is to put a fluorescent

material over the reactants within the biochip and to utilize a scanner having a PMT

(Photomultiplier tube) sensor for detecting a specific wavelength of light emitted from the

fluorescent material when it is excited by a specific wavelength of light. The PMT sensor

is a device for determining the intensity of incident light. The PMT sensor produces an

output current in proportion to the intensity of the incident light. The PMT sensor is so

highly sensitive that is able to count each photon of the incident light.

Because the scanner utilizes the PMT sensor that can detect only one point, the

biochip can be diagnosed by being moved (on a single-axis stage) a certain distance in one

direction,, and having the PMT sensor move in a reciprocal fashion. That is, the scanner does not function an automatic diagnosing device for detecting disease, but as a device for

acquiring data as would a microscope.

There are various kinds of devices for diagnosing disease by detecting a specific

wavelength light emitted from fluorescent material that is excited by a specific wavelength

of light: Abbott Diagnostics' AxSYM, Bayer's Immuno-1, Beckman Coulter's Access,

Boehringer Mannheim's Elecsys, Chiron's ACS: 180 SE and Centaur, Dade's Opus Plus,

Diagnostic Products' Immulite and Immulite 2000, Nichols' Advantage, Ortho

Diagnostics' Vitros, Toshoh's AIA-1200 and NexIA. These devices use a well plate, a

cubed-type tube, or a sheet.

Conventional scanners utilizing a PMT sensor have a weakness: it takes 3 to 5

minutes to acquire data due to the operation characteristics of the scanner.

Also, the conventional scanner utilizing a PMT sensor are again weak because

they are complicated, precision is required to operate them successfully, and careful

maintenance is required to achieve optimum results.

Also, the conventional scanner utilizing a PMT sensor has a problem in that

contamination can take place on the medical testing samples.

Further, it is impossible for a diagnosing device using a well plate, cubed-type tube

or sheet to diagnose multiple medical testing samples in one operation. DISCLOSURE OF THE INVENTION

It is a primary object of the present invention to provide a biochip reader that can

quickly determine whether or not the infection of disease is present by diagnosing a

medical testing sample arrayed on a biochip.

It is another object of the present invention to provide a biochip reader that can

diagnose multiple medical testing samples on biochips and determine whether or not the

infection of disease is present.

It is yet still another object of the present invention to provide a biochip reader that

can diagnose medical testing samples using an optical sensor.

Yet still another object of the present invention is to provide a biochip reader that

can recognize an optical identification code adhered to a biochip and automatically

diagnose the biochip by analyzing information retrieved from a database that corresponds

to the recognized optical identification code.

To achieve the above-mentioned objectives, according to one aspect of the

preferred embodiment of the present invention, a biochip reader for diagnosing medical

testing samples on a biochip, which contains an optical identification code, the biochip

reader comprising: a light source part for emitting light, an excitation filter part having a

first filter for exciting the emitted light to a first wavelength of light, wherein the excitation

filter equipment comprises at least one filter, a stage part for supporting the biochip, an

absorption filter part having a second filter for absorbing a second wavelength of light excited to be reflected onto the medical testing samples, wherein the absorption filter

equipment comprises at least one filter, an optical sensor part for abstracting an image

signal by recognizing the second wavelength of light, an optical identification code

interpreter for inteφreting the optical identification code and a central controller for

receiving the optical identification code from the optical identification code inteφreter, for

controlling the light source, the excitation filter part, the stage part and absoφtion filter

part in accordance with biochip information that corresponds to the optical identification

code and is stored in a database and for diagnosing the medical testing samples with the

image signal from the optical sensor part in accordance with the biochip information, can

be provided.

In the preferred embodiment, the biochip information comprises at least one of a

medical sample type, a medical sample region, a medical sample region location, a medical

sample array, a medical sample content, a medical sample size, a medical sample interval,

light intensity controlling quantity, a excitation filter type, an absoφtion filter type, a scale

conversion controlling quantity, a shutter controlling quantity and a stage controlling

quantity

In another preferred embodiment, the central controller controls the light source

part by utilizing the light intensity controlling quantity, the excitation filter part by utilizing

the excitation filter type, the stage part by utilizing the stage controlling quantity and the

absoφtion filter part by utilizing the absoφtion filter type. In another preferred embodiment, the biochip reader further comprises a scale

conversion driver for converting scales corresponding to the medical testing sample,

wherein the central controller controls the scale conversion driver by utilizing the scale

conversion controlling quantity.

In another preferred embodiment, the optical identification code is a bar code or a

reference spot.

According to another aspect of the preferred embodiment of the present invention,

is a method for diagnosing medical testing samples on a biochip in a biochip reader

comprising a light source, an excitation filter part, an absoφtion filter part, an optical

sensor part and an optical identification code inteφreter, wherein the biochip contains an

optical identification code, the method comprising the steps of: receiving the optical

identification code recognized by the optical identification code inteφreter, abstracting

biochip information that corresponds to the optical identification code and is stored in a

database, controlling a light source, an excitation filter part, an absoφtion filter part and an

optical sensor part in accordance with the abstracted optical identification code, receiving

an image signal from the optical sensor part according to the result of the control, and

diagnosing the medical testing samples by utilizing the received image signal, is provided.

sample array, a medical sample content, a medical sample size, a medical sample interval, light intensity controlling quantity, a excitation filter type, an absorption filter type, a scale

quantity.

In another preferred embodiment, the light source part is controlled by the use of

the light intensity controlling quantity, the excitation filter part is controlled by the use of

the excitation filter type, the stage part is controlled by the use of the stage controlling

quantity and the absoφtion filter part is controlled by the use of the absoφtion filter type.

In another preferred embodiment, the biochip reader further comprises a scale

conversion driver for converting scale corresponding to the medical testing sample,

wherein the scale conversion driver is controlled by the use of the scale conversion

controlling quantity.

reference spot.

a method for diagnosing medical testing samples on a biochip, the method comprising the

steps of: receiving an image signal corresponding to the medical testing samples from an

optical sensor, executing a background image subtraction and a black level subtraction on

the image signal, producing a spot intensity corresponding to the medical testing samples,

normalizing the spot intensity by the use of a pre -produced reference spot intensity and

determining whether the medical testing samples are positive or negative by the use of the normalized spot intensity, is provided.

In the preferred embodiment of the present invention, the method further

comprises the step of arraying automatically and distinguishing the medical testing

samples by utilizing the reference spot intensity, wherein the step of arraying automatically

and distinguishing the medical testing samples by utilizing the reference spot intensity is

the step of abstracting selectively a plurality of reference spots by utilizing the reference

spot intensity, and then on the basis of the specially-shaped array of the plurality of

reference spots, arraying and distinguishing the medical testing samples by abstracting

their origin and direction.

In another embodiment of the present invention, the reference spot intensity

comprises at least one of an absolute positive intensity and an absolute negative intensity,

and the step of normalizing the spot intensity uses the following:

where, I_n is a normalized spot intensity,

I is a spot intensity before normalization,

I₍₊₎ is an absolute positive intensity,

I₍.₎ is an absolute negative intensity,

ai, a₂, a₃, and a₄ are normalization coefficients, and

K is a normalization range coefficient. In another preferred embodiment, the step of determining whether the medical

testing samples are positive or negative by utilizing the normalized spot intensity must

follow that when the normalized spot intensity is more than a predetermined cutoff,

determining positive and when the normalized spot intensity is less than a predetermined

cutoff, determining negative, wherein the predetermined cutoff is between the absolute

positive intensity and the absolute negative intensity.

is a method for diagnosing a progression of a disease utilizing medical testing samples on a

biochip, the method comprising the steps of: abstracting a spot intensity pattern that

corresponds to the medical testing samples according to wavelengths utilizing a plurality of

filters, wherein the plurality of filters each excite specific wavelengths of light; comparing

the abstracted spot intensity pattern to a predetermined pattern; determining the

progression of a disease or producing information that is utilized to determine the

progression of a disease utilizing the comparison, is provided.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG 1 is a cross-sectional view showing the spot to be inteφreted in the biochip

reader in accordance with the preferred embodiment of the present invention;

FIG 2 is a cross-sectional view showing an internal structure of the biochip reader

in accordance with the preferred embodiment of the present invention; FIG 3 is a block diagram of the biochip reader in accordance with another

preferred embodiment of the present invention;

FIG 4 shows a biochip in accordance with the preferred embodiment of the present

invention;

FIG 5 a is an ER (entity -relationship) diagram showing the structure of a database

in accordance with the preferred embodiment of the present invention;

FIG 5b shows exemplary field values of the database shown in FIG 5a in

accordance with the preferred embodiment of the present invention;

FIG 6 shows a biochip marked with a reference spot in accordance with the

preferred embodiment of the present invention;

FIG 7a is a flowchart for seeking the location of each reference spot in accordance

with the preferred embodiment of the present invention;

FIG 7b shows the positional relationship between each reference spot in

accordance with the preferred embodiment of the present invention;

FIG 8 shows the internal structure of a central controller in accordance with the

preferred embodiment of the present invention;

FIG 9 shows the external appearance of an excitation filter wheel or an absoφtion

filter wheel;

FIG 10 is a flowchart for illustrating a black-level subtraction. <The description of the reference characters of the major parts of the drawings---

101 ^• optical sensor part 109- ^{• •} absorption filter part

115 "^•magnification/retrenchment part 123 "-object lens part

125-"bar code inteφreter 127--stage part

133 ^{• •}excitation filter part 139 ^{• • •}light source

301 ^{• • •} central controller

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

Hereinafter, the preferred embodiment of the present invention will be described

with accompanying drawings.

In one preferred embodiment of the present invention, a biochip comprises any

biological chip, such as a DNA chip, a protein chip or an RNA chip. However, we define

the protein chip for the puφose of the description.

In one preferred embodiment of the present invention, we define an optical

identification code as a bar code for the puφose of the description. Herein the optical

identification code is an optically discemable mark on a biochip that directly or indirectly

represents information. The optical identification code comprises at least one barcode and

one reference spot.

The process of producing and utilizing a biochip is as follows:

First, the first protein chip is generated by dotting an antigen in a chipmaker's biochip arrayer. Next, the first protein chip is fixed within a chamber in which the

temperature and humidity are maintained thereinafter. On the first protein chip, each spot

can be an identical antigen or a different antigen. For example, on the first protein chip,

one part may be for an HIV antigen, another part may be for an HBV antigen and the other

part may be for an HCV antigen.

The first protein chip is delivered to customers in hospitals, etc. Customers

generate the second protein chip by dotting an antigen comprised of the blood or humors

(body fluids) of a subject to be measured on the first protein chip in a customer's biochip

arrayer. At this time, the spot of the pre-produced protein chip must correspond with the

customer's spot in the customer's biochip arrayer. That is, it is important to precisely dot

an antigen to a corresponding spot on the first protein chip. Cause the reaction of the

second protein chip in a reactor afterward.

Then, a user puts the reacted second protein chip into the biochip arrayer again and

dots the second antigen, coupled to FITC (fluorescenin isothiocyanate), to the second

protein chip. This time, a precise relocation is required.

FIG 1 shows a cross-sectional view of the spot to be inteφreted in the biochip

reader in accordance with the preferred embodiment of the present invention;

Referring to FIG 1, as described above, after dotting an antigen 104 (for example,

HIV, HCV, and so on) onto a biochip substrate 102 (for example, a glass slide) in a

chipmaker's biochip arrayer, then dot an antigen 106 comprised of blood or humors in a customer's biochip arrayer. Then, dot the second antigen 108 coupled with the FITC.

Then, diagnose by using a biochip reader to detect the result of the reaction.

FIG 2 is a cross-sectional view showing the internal structure of a biochip reader

in accordance with the preferred embodiment of the present invention.

Referring to FIG 2, the biochip reader comprises an optical sensor part 101, an

absoφtion filter part 109, a magnification/retrenchment part 115, an object lens part 123, a

barcode inteφreter 125, a stage part 127, an excitation filter part 133 and a light source

partl39.

The optical sensor part 101 comprises an optical sensor 103 similar to that of a

CCD camera, especially a cooled CCD camera, for grasping an image signal, a shutter 105

and a shutter driver 107 for driving the shutter 105.

The absoφtion filter part 109 comprises an absoφtion filter wheel 113 for

installing a plurality of absoφtion filters (not shown) and an absoφtion filter wheel driving

motor 111. The usage of the absoφtion filter (not shown) will be described later with

drawings along with the absoφtion filter wheel 113 and the function of the absorption

filter wheel driving motor 111.

The magnification/retrenchment part 115 comprises a zoom lens 121, a zoom belt

119 for controlling the zoom lens 121 and a zoom motor 117 for driving the zoom belt 119.

The zoom motor 117 operates the scale conversion of the zoom lens 121.

The stage part 127 comprises a stage 131 on which to place the biochip 124 and a stage driving motor 129 for driving the stage 131. An aperture is formed at the place of the

stage part 127 where the biochip 124 is to be inteφreted.

The bar code inteφreter 125 recognizes a bar code adhered to a grip of the biochip

124. The bar code inteφreter 125 can be moved by a bar code inteφreter driving motor

(not shown). The bar code inteφreter 125 makes an inteφretation of the adhered bar code

and transmits the result of inteφretation to a central controller (not shown). According to

another preferred embodiment of the present invention, the bar code inteφreter 125 can be

attached to or detached freely from the biochip reader.

The excitation filter part 133 operates to excite a light from the light source part

139 to a filter (not shown) corresponding to a specific wavelength and comprises an

excitation filter wheel 137 for installing a plurality of excitation filters and an excitation

filter wheel driving motor 135 for driving the excitation filter wheel 137.

The light source part 139 comprises a light source 149, a luminosity controller 145

for controlling the luminosity of the light emitted from the light source 149, a luminosity

controller driving motor 147 for driving the luminosity controller 145, a collimator 143 for

uniformly irradiating the place on the biochip 124 to be putted upon and a total reflecting

mirror 141 for totally reflecting the light from the collimator 143.

The optical sensor part 101, the shutter 105, the absoφtion filter (not shown)

corresponding to the bar code in the absoφtion filter wheel 113, the zoom lens 121, the

object lens 123, the biochip 124, the aperture in the stage part 131, the excitation filter (not shown) corresponding to the barcode in the excitation filter wheel 137 and the total

reflection mirror 141 must be optically arranged.

FIG 3 is a block diagram of the biochip reader in accordance with another

preferred embodiment of the present invention;

Referring to FIG 3, the biochip reader comprises a bar code inteφreter 125 for

recognizing a bar code identifier from the bar code adhered to the biochip and a central

controller 301.

The central controller 301 receives the bar code identifier from the bar code

inteφreter 125 and according to stored biochip information, transmits a control signal,

corresponding to the bar code identifier, to the shutter driver 107, the absoφtion filter

wheel driving motor 111, the scale conversion driver 303, the stage driving motor 129, the

excitation filter wheel driving motor 135 and the luminosity controller driving motor 147.

Also, the central controller 301 processes an inteφretation of an image signal

corresponding to the medical testing samples received from the optical sensor 103 and then

determines existence or nonexistence of a disease.

invention;

Referring to FIG 4, the biochip is formed with a grip region 401 and a medical

spot region 405 and dotted with a medical testing sample. Hereinafter we use the medical

spot and the medical testing sample together. In the grip region 401, a bar code corresponding to the biochip 403 is adhered. The

bar code 403 comprises a biochip identifier predetermined by a biochip manufacturer and a

biochip customer. Because biochip information according to the biochip identifier is stored

in a database in advance, subsequently, the barcode inteφreter 125 in FIG 2 recognizes the

biochip identifier, then biochip information according to the biochip identifier can be

abstracted from the database. Hereinafter the description assumes that the database stores

the biochip information and a patient information database stores the patient information.

However, the patient information can be stored at the database.

The medical spot region 405 of the biochip is dotted with medical spots. The

contents of the medical spots can be identical. The medical spot region 405, however, can

preferably be comprised of a plurality of regions with each region being dotted with

different contents.

The reference character 407 illustrates a medical spot dotted with a substance

uniquely distinguishable from the contents of the other spots.

We describe the method used for controlling the biochip reader using interpreted

information from the bar code inteφreter 125 in FIG 2 with an example.

At first, if a bar code identification code recognized by the bar code inteφreter 125

in FIG 2 is 13-0343-34, the first two digits 13 represent the biochip identifier and the other

digits 0343-34 represent a patient identifier coupled to the patient information database.

When a biochip is produced in the chipmaker's biochip arrayer, the bar code identification code 13-03430-34 is adhered to the biochip substrate. Using the biochip

identifier 13 to represent the composition of the biochip, the biochip information can be

searched from the database as described later by FIG 5a and FIG 5b.

After dotting the first biochip acquired from the customer's biochip arrayer with

an antigen corresponding to a specific patient, then generate a patient information database

corresponding to the patient information identifier, that being the last digits of the bar code

identification code 0343-34. For example, a database file name is 0343-34.dat, generated

on 3 NOV 2000, and identifying 100 persons (PFC Al Pacino and Coφoral Robert De Niro

are included in this 100 persons) of 1st squad in 1323 infantry unit can be stored in this file.

The bar code identification code 13-0343-34 is adhered to the biochip substrate

recognized in the biochip reader. Then, abstract the biochip information corresponding to

the biochip identifier 13 from the pre-constructed database (similar to a chipmaker's

database) and diagnose the biochip according to the biochip information. In this case, of

course, search the patient information corresponding to the patient information identifier

0343-34 from the patient information database.

By way of the aforementioned steps, we can have the result that PFC Al Pacino is

negative for HCV and HIV and Coφoral Robert De Niro is positive for HCV and negative

for HIV.

FIG 5a is an ER (entity-relationship) diagram showing the structure of a database

in accordance with the preferred embodiment of the present invention; Referring to FIG 5a, the database can comprise a biochip identifier 501 field, a

spot type 503 field, a spot region 505 field, a spot region location 507 field, a spot array

509 field, a spot content 511 field, a spot size 513 field, a spot interval 515 field, a

luminosity controlling quantity 517 field, an excitation filter type 519 field, an absorption

filter type 521 field, a scale conversion controlling quantity 523 field, a shutter controlling

quantity 525 field and a stage controlling quantity 527 field. However, the fields

comprising the database are not limited to these fields.

The spot region and locations of each spot can be produced from the location of

the reference spot. The location of the reference spot is a reference indication marked on

the biochip, or information on the reference spot dotted onto the biochip.

The content of the reference spot dotted onto the biochip is preferably an absolute

positive or an absolute negative.

By the use of the reference spot, locations of each spots can be recognized.

Locations of each spots can be recognized using FIG 6, FIG 7a and FIG 7b. The

recognition of the locations of each spot is merely an example and it is also appreciated

that other methods can be applied without departing from the spirit and the scope of the

present invention.

FIG 6 shows a biochip marked with a reference spot in accordance with the

preferred embodiment of the present invention;

Referring to FIG 6, three reference spots 603, 605, 607 are marked on the biochip 124. Herein the intermediate reference spot 603 is recognized as a center reference spot

and other spots 605, 607 are set to x-axis and y-axis respectively.

with the preferred embodiment of the present invention;

FIG 7b shows the positional relationship between each reference spot in

accordance with the preferred embodiment of the present invention;

Referring to FIG 7a and 7b, at step 701, recognize a reference spot marked in the

biochip.

Then, at step 703, produce locations of the reference spot Rl 603, R2 607 and R3

605.

Using the locations of each reference spot Rl 603, R2 607 and R3 605, at step 705,

produce the coordinates of the origin, the unit vector of the X-axis and the unit vector of

the Y-axis.

Ox, x coordinate of the origin, can be produced by formula 1 and Oy, y coordinate

of the origin, can be produced by formula 2.

FORMULA 1

Ox = Rl.x

FORMULA 2

Oy = Rl.y

Ex, the unit vector of X-axis, can be produced by formula 3 and Ey, the unit vector of Y-axis X, can be produced by formula 4.

FORMULA 3

Ex R3-R1

\m-κι\

FORMULA 4

Ey R - JRi

\m-

Using the produced coordinates of the origin, the unit vector of the X-axis (Ex)

and the unit vector of the Y-axis (Ey), at step 707, the real coordinate (Px, Py) on the array

of the spot location (X, Y) is produced by formula 5 and formula 6.

FORMLUA 5

Px = Ox + X*Ex

FORMULA 6

Py = Oy + Y*Ey

Preferably the reference spot location (X, Y) can be stored in advance under the

terms of an agreement between the chipmaker and the customer.

At step 709, a numerical control code for controlling each device is generated in

the central controller using the real coordinates.

FIG 5b shows optimal field values of the database shown in FIG 5a in accordance

with the preferred embodiment of the present invention; Referring to FIG 5b, the biochip identifier 501 is 13, the spot type 503 is HCV and

HIV, the spot region 505 is in a 1, 2 divisional mode, the first location of the spot region

507 is (10, 10) and the second location of the spot region 507 is (10, 100), the first location

of the spot array 509 is 10*10 and the second location of the spot array 509 is 8*8, the spot

content 511 of the first location is HCV and the spot content 511 of the second location is

HIV, the spot size 513 of the first location is 500j--m and the spot size 513 of the second

location is 500μm, the spot interval 515 of the first location is 100 μ and the spot interval

515 of the second location is 100j-m, the luminosity controlling quantity 517 of the first

location is 80 % and the luminosity controlling quantity 517 of the second location is 90 %,

the excitation filter type 519 of the first location is GREEN and the excitation filter type

519 of the second location is RED, the absoφtion filter type 521 of the first location and

the second location are BLUE, the scale conversion controlling quantity 523 of the first

location is 10 times and the scale conversion controlling quantity 523 of the second

location is 15 times, the shutter controlling quantity 525 of the first location is 20 seconds

and the shutter controlling quantity 525 of the second location is 40 seconds and the stage

controlling quantity is to move to the second location from the first location.

Referring to FIG 3 again, using the biochip information stored in the database

corresponding to the above-mentioned bar code, the central controller 301 can produce and

transmit a control signal to each device.

The shutter driver 107 can be operated by responding to the control signal received from the central controller 301, however, it can be operated manually in another preferred

embodiment of the present invention.

In the preferred embodiment of the present invention, the optical sensor can be a

CCD camera.

In the CCD camera, as an integrated form of microscopic pixels, CCD can change

the light received through each lens into a charge and store the charge within itself. That is,

each pixel has the function of a condenser. Accordingly, corresponding to the locations and

quantities of each pixel, data describing brightness can be acquired. The method for

displaying colors in CCD is to utilize a color filter. Two methods using color filters

comprised of four colors make up one set. In the primary colors system, G-R-G-B (Green-

Red-Green-Blue) is used and in the complementary colors system, C-M-Y-G (Cyan-

Magenta-Yellow-Green) is used.

There are two scan methods of the CCD, an interlaced scan and a progressive scan.

In the interlaced scan method, an image is scanned in twice. Herein 'scan' means to output

the stored charge. In the progressive scan method, all pixels are scanned at one time.

Generally, in the case of the optical sensor (having over 350,000 pixels) the progressive

scan method is used.

Hereinafter we describe by example each method for controlling.

FIG 11 shows a luminosity controller in accordance with the preferred

embodiment of the present invention. Referring to FIG 11, the luminosity controller comprises a MMC board 1101

(Multi-Motion Control) coupled to the central controller 301, a step motor driver 1103, a

step motor 1105 and a filter 1107. The step motor driver 1103 corresponds to the

luminosity controller driving motor 147 and the step motor 1103 corresponds to the

luminosity controller 145. When the central controller 301 transmits a quantity of pulses

corresponding to the controlling quantity stored in advance to the step motor driver 1103

through the MMC board 1101, the step motor driver operates the step motor by generating

a pulse according to the aforementioned quantity of pulses. The filter 1107 starts to rotate

by the operation of the step motor 1105. The level of luminosity according to the rotational

angle of the filter 1107 will be described by FIG 12.

FIG 12 shows the level of the luminosity according to the rotational angle of the

filter.

Referring to FIG 12, there is an example of the level of the luminosity according to

the each angle.

A quantity of pulses corresponding to the controlling quantity stored in advance is

shown in FIG 13. As described above, the quantity of pulses in FIG 13 illustrates an

example wherein the biochip identifier of the biochip identification code is 13. For

example, as aforementioned, the luminosity controlling quantity 517 corresponding to

the case wherein the biochip identifier is 13 is 80 % at the first location and 90% at the

second location. When the central controller 301 applies 225 pulses corresponding to the controlling quantity 80% at the first location to the MMC board 1101, by the

aforementioned method, the step motor 1105 rotates by 112.5° corresponding to the 225

pulses. Herein the step motor 1105 is first initialized and then the aforementioned

method is applied. Also, the step motor 1105 preferably memorizes the quantity of

pulses corresponding to the present position. In this case, because the present controlling

quantity is 80%, the step motor memorizes 225 as the quantity of pulses. Because the

controlling quantity corresponding to the second location is 90 % and corresponding

quantity of pulses is 135, so, if -90 is applied, then the quantity of pulses being 135 is

applied to the present quantity of pulses being 225.

The method for controlling the excitation filter and the absoφtion filter is similar

to the aforementioned method for controlling the luminosity. Accordingly, we omit the

description of excitation filter. Suffice it to state, the filter types and the corresponding

quantity of pulses are stored in advance. The quantities of pulses corresponding to the

stored controlling quantity are shown in FIG 15 and the types of filters 1401 are shown

in FIG 14. In the case wherein the biochip identifier of the bar code identification code

is 13, the corresponding excitation filter type 519 of the first location is GREEN and the

excitation filter type 519 of the second location is RED, the corresponding absoφtion

filter types 521 of the first location and the second location are BLUE. An excitation

filter and an absoφtion filter corresponding to the first location are 7 and 6 respectively,

and an excitation filter and an absoφtion filter corresponding to the second location are 5 and 6 respectively. Accordingly, for example, the absoφtion filter at the first location,

when the central controller 301 applies the quantity of pulses being 495 corresponding

to the absoφtion filter type 6 to the MMC board 1101, then by the aforementioned

method, the step motor 1105 rotates by 247.5° corresponding to the quantity of pulses

being 495. Because the absorption filter rotates by 247.5° due to the step motor 1105,

the BLUE filter is selected.

FIG 16 shows the scale conversion device in accordance with the preferred

embodiment of the present invention.

Referring to FIG 16, the scale conversion device comprises a step motor driver

(not shown) coupled to a MMC board (not shown), a step motor 117 for operating as a

zoom motor, a zoom belt 119, a zoom lens 121, an object lens 123 and a camera 103

functioning as an optical sensor. The quantities of pulses stored in advance are shown in

FIG 17. As described above, the quantities of pulses in FIG 16 are given to illustrate an

example wherein the biochip identifier of the biochip identification code is 13. As in the

aforementioned example, the ratio of the scale conversion controlling quantity

corresponding to biochip identifier 13 is 10 times at the first location and 15 times at the

second location and these quantities correspond respectively to the quantity of pulses 40

and 80. Because the rotation of the step motor 117 according to the quantity of pulses is the

same as described above, we omit the description here. Herein the zoom lens 121 moves

up and down according to the rotation of the step motor 117 in the process of converting rotational motion into rectilineal motion. For this reason, the distance between the camera

103 and interim lens 1601 can be changed.

The method for controlling the shutter can be accomplished by using a general

shutter driver. The general shutter driver comprises a spring and an electromagnet. The

shutter is closed by way of the spring and when a current is applied to the electromagnet,

the shutter remains open, and when the applied current is cut off, then the shutter is closed

by the tension of the spring. Because a conventional camera includes a function of

controlling the exposure time, the exposure time corresponding to biochip identifier 13 is

20 seconds at the first location and 40 seconds at the second location.

The method for controlling the stage is similar to the aforementioned control

methods. That is, according to the controlling quantities stored in advance, the step motor

driver and the step motor are operated toward X direction and Y direction through the

MMC board. So, we omit a detailed description of this.

preferred embodiment of the present invention;

Referring to FIG 8, the central controller 301 comprises an I/O interface 803 for

receiving the bar code identifier from the bar code inteφreter 125 and the image signal

from the optical sensor 103 and for transmitting control signals to each device, a

database 805 for storing biochip information, a processor 801 for generating the

controlling signals using the biochip information, recognizing the image signal, determining existence and nonexistence of a disease and then producing information

about the progression of a disease.

FIG 9 shows the external appearance of an excitation filter wheel or an absorption

filter wheel;

Referring to FIG 9, a plurality of apertures 901 for installing a plurality of

excitation filters or absoφtion filters are formed on the excitation filter wheel or the

absoφtion filter wheel.

Hereinafter we describe the method for recognizing the image corresponding to

the image signal received using the aforementioned method.

At first, a background image subtraction is executed on the image.

The background image subtraction is a method for eliminating the background

noise by subtracting a pre-stored image of the biochip substrate (background image) dotted

with no medical samples from the image.

Also, in the same manner as the background subtraction, to improve the reliability

of image data, a black level subtraction is executed.

FIG 10 is a flowchart for illustrating a black-level subtraction.

Referring to FIG 10, step 1001 shows the state of closing the shutter and then, at

step 1003, a black level image is acquired by photography and subsequently stored.

After that, at step 1005, the shutter is opened and then, at step 1007, a real image is

acquired by photography and subsequently stored. After that, at step 1009, a black level subtraction is executed by subtracting the

black level image from the real image.

Hereinafter we describe the method for abstracting a spot intensity.

At first, the edges of each spot are abstracted. There are several methods for

abstracting edges such as by using a sub-pixel algorithm, an optimal threshold selection

algorithm, or a local intensity gradient algorithm. At least one algorithm from among the

group consisting of the above-mentioned algorithms can be applied to the preferred

embodiment of the present invention as an algorithm for abstracting an edge.

After that, the internal area of the abstracted edge is produced and intensities of

each pixel within the abstracted edge are added together.

Finally, dividing the added intensity by the area produces a spot intensity.

Hereinafter we describe the processed image signal method used for diagnosing.

At first, the intensity of the reference spot is produced using the above-mentioned

method. There are two kinds of reference spots, an absolute positive spot and an absolute

negative spot. The quantity of the spot intensity of each biochip can vary according to

external factors such as photo-oxidization, and so on. Accordingly, it is preferable to dot

the absolute positive spot and the absolute negative spot together. Then, using the absolute

positive intensity and the absolute negative intensity as references, normalize each spot

according to formula 7. FORMULA 7

where, In is a normalized spot intensity, I is a spot intensity before normalization,

I₍₊₎ is an absolute positive intensity, I₍-₎ is an absolute negative intensity, aj, a₂, a₃, and a₄

are normalization coefficients, and K is a normalization range coefficient.

Because the most important thing in the process of making a diagnosis is the

interval between the absolute positive intensity and the absolute negative intensity,

remember to set the absolute intensity at 100 and the absolute intensity at 0.

Correspondingly, always determine as positive when the normalized intensities of each

spot are more than 100 and always as negative when the normalized intensities of each

spot are less than 0. If a spot intensity exists between the absolute positive intensity and the

absolute negative intensity, determine whether the spot intensity is positive or negative by

implementing a cutoff value acquired from clinical testing.

Also, it is possible to determine the progression of a disease by using the biochip

reader in accordance with the preferred embodiment of the present invention.

More particularly, determining the progression of a disease can be accomplished

by comparing a plurality of intensity patterns according to various wavelengths by using

various kinds of filters with pre-built patterns. Also, information derived from a

comparison result is useful for determining the progression of a disease. Also, the capacity of the light source can be tested in the biochip reader in

accordance with the preferred embodiment of the present invention.

More particularly, after removing the absorption filter and then the excitation filter

from the absoφtion filter wheel and the excitation filter wheel respectively, then a filter

having the smallest transmissivity is inserted into the wheel of the luminosity controller.

After acquiring a background image, by irradiating for a fixed exposure time to produce a

background image of average intensity, then, if the average intensity is over a certain

standard, determine that the light source is suitable or, alternately, change the light source.

It is appreciated for those skilled in the art that the present invention is not limited

to the aforementioned embodiments in the detailed descriptions, the appended claims or

the appended drawings, and a plurality of modifications can be accomplished within the

spirit and scope of the present invention.

Industrial Applicability

According to the present invention, a biochip reader that can quickly determine

whether or not a disease is present by diagnosing a medical testing sample arrayed on a

biochip is provided.

According to the present invention, a biochip reader that can rapidly diagnose

multiple medical testing samples fixed to biochips and determine whether or not a disease

is present, is provided. According to the present invention, a biochip reader that can diagnose medical

testing samples using an optical sensor is provided.

According to the present invention, a biochip reader that can recognize an optical

identification code adhered to a biochip and automatically diagnose the biochip using

biochip information stored in a database that corresponds to the optical identification

code, is provided.

Claims

1. A biochip reader for diagnosing medical testing samples on a biochip, having

an optical identification code within itself, said biochip reader comprising:

a light source part for emitting light;

a excitation filter part having a first filter for exciting the emitted light to a first

wavelength of light, wherein said excitation filter part comprises at least one filter;

a stage part for supporting said biochip;

an absoφtion filter part having a second filter for absorbing a second wavelength

light excited to be reflected onto the medical testing samples, wherein said absoφtion filter

equipment comprises at least one filter;

an optical sensor part for abstracting an image signal by recognizing the second

wavelength of light;

an optical identification code inteφreter for interpreting the optical identification

code; and

a central controller for receiving the optical identification code from said optical

identification code interpreter,

for controlling said light source, said excitation filter part, said stage part and said

absoφtion filter part in accordance with biochip information that corresponds to the optical

identification code and is stored in a database and

for diagnosing the medical testing samples utilizing the image signal from said optical sensor part in accordance with the biochip information.

2. The biochip reader as stated in claim 1, wherein the biochip information

comprises at least one of a group consisting of a medical sample type, a medical sample

region, a medical sample region location, a medical sample array, a medical sample content,

a medical sample size, a medical sample interval, a light intensity controlling quantity, an

excitation filter type, an absoφtion filter type, a scale conversion controlling quantity, a

shutter controlling quantity, and a stage controlling quantity.

3. The biochip reader as stated in claim 2, wherein said central controller controls

said light source part by utilizing the light intensity controlling quantity.

4. The biochip reader as stated in claim 2, wherein said central controller controls

said excitation filter part by utilizing the excitation filter type.

5. The biochip reader as stated in claim 2, wherein said central controller controls

said stage part by utilizing the stage controlling quantity.

6. The biochip reader as stated in claim 2, wherein said central controller controls

said absoφtion filter part by utilizing the absoφtion filter type.

7. The biochip reader as stated in claim 2, further comprising:

a scale conversion driver for converting a scale corresponding to the medical

testing sample.

8. The biochip reader as stated in claim 7, wherein said central controller controls

said scale conversion driver by the use of the scale conversion controlling quantity.

9. The biochip reader as stated in claim 1, wherein the optical identification code is

a bar code or a reference spot.

10. A method for diagnosing medical testing samples on a biochip utilizing a

biochip reader comprising: a light source, an excitation filter part, an absoφtion filter part,

an optical sensor part and an optical identification code inteφreter, wherein said biochip

has an optical identification code within itself, and said method comprising the steps of:

receiving the optical identification code recognized by the optical identification

code inteφreter;

abstracting biochip information that corresponds to the optical identification code

and is stored in a database;

controlling a light source, an excitation filter part, an absoφtion filter part and an

optical sensor part in accordance with the abstracted optical identification code; receiving an image signal from the optical sensor part according to the result of the

control; and

diagnosing the medical testing samples by utilizing the received image signal.

11. The method as stated in claim 10, wherein the biochip information comprises

at least one of a group comprised of a medical sample type, a medical sample region, a

medical sample region location, a medical sample array, a medical sample content, a

medical sample size, a medical sample interval, a light intensity controlling quantity, an

shutter controlling quantity and a stage controlling quantity.

12. The method as stated in claim 11, wherein the light source part is controlled by

the use of the light intensity controlling quantity.

13. The method as stated in claim 11, wherein the excitation filter part is

controlled by the use of the excitation filter type.

14. The method as stated in claim 11, wherein the stage part is controlled by the

use of the stage controlling quantity.

15. The method as stated in claim 11, wherein the absoφtion filter part is

controlled by the use of the absoφtion filter type.

16. The method as stated in claim 11, wherein the biochip reader further comprises

a scale conversion driver for converting a scale corresponding to the medical testing

sample.

17. The method as stated in claim 16, wherein the scale conversion driver is

controlled by the use of the scale conversion controlling quantity.

18. The method as stated in claim 10, wherein the optical identification code is a

bar code or a reference spot.

19. A method for diagnosing medical testing samples on a biochip, said method

comprising the steps of:

receiving an image signal corresponding to the medical testing samples from an

optical sensor;

executing a background image subtraction and a black level subtraction on the

image signal;

producing a spot intensity corresponding to the medical testing samples; normalizing the spot intensity by the use of a pre-produced reference spot

intensity; and

determining whether the medical testing samples are positive or negative by

utilizing the normalized spot intensity.

20. The method as stated in claim 19, wherein the method further comprises the

step of:

automatically arraying and distinguishing the medical testing samples by utilizing

the reference spot intensity.

21. The method as states in claim 20, wherein the step of automatically arraying

spot intensity, then on the basis of the specially-shaped array of the plurality of reference

spots, arraying and distinguishing the medical testing samples by abstracting the origin and

direction of the array of the medical testing samples.

22. The method as stated in claim 19, wherein the reference spot intensity

comprises at least one of an absolute positive intensity and an absolute negative intensity.

23. The method as stated in claim 22, wherein the step of normalizing the spot

intensity is the step of utilizing the following:

where, In is a normalized spot intensity,

I is a spot intensity before normalization,

I₍₊₎ is an absolute positive intensity,

I₍.₎ is an absolute negative intensity,

ai, a₂, a₃, and a₄ are normalization coefficients, and

K is a normalization range coefficient.

24. The method as stated in claim 22, wherein the step of determining whether the

medical testing samples are positive or negative by utilizing the normalized spot intensity

is the step wherein when the normalized spot intensity is more than a predetermined cutoff,

determining a positive value and wherein when the normalized spot intensity is less than a

predetermined cutoff, determining a negative value, and wherein the predetermined cutoff

is between the absolute positive intensity and the absolute negative intensity.

25. A method for diagnosing a progression of a disease by utilizing medical testing

samples on a biochip, said method comprising the steps of: abstracting a spot intensity pattern that corresponds to the medical testing samples

according to a wavelength by utilizing a plurality of filters, wherein the plurality of filters

each excite a specific wavelength of light;

comparing the abstracted spot intensity pattern with a predetermined pattern;

determining the progression of a disease or producing information that is utilized

to determine the progression of a disease by a comparison.