CN1255671C - Multiple-marknig-object biological chip signal analyzing systems - Google Patents

Multiple-marknig-object biological chip signal analyzing systems Download PDF

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CN1255671C
CN1255671C CNB021363706A CN02136370A CN1255671C CN 1255671 C CN1255671 C CN 1255671C CN B021363706 A CNB021363706 A CN B021363706A CN 02136370 A CN02136370 A CN 02136370A CN 1255671 C CN1255671 C CN 1255671C
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CN1472527A (en
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胡赓熙
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Shanghai Changrun Biotechnology Co ltd
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SHUKANG BIO-TECHNOLOGY Co Ltd SHANGHAI
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Priority to PCT/CN2003/000123 priority patent/WO2004013627A1/en
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Abstract

The present invention relates to a multi-marker biochip signal analysis system which comprises an image collection system, an image processing system and a data analysis and output system. The analysis system of the present invention serves as a matched analysis system of a biochip detection system, when the reaction of the biochip detection system is completed, a luminescent signal is generated on a specific position on the chip; a refrigeration type CCD (cool CCD) is used for simultaneously shooting light signals on a plurality of biochips, and the light signals are converted into image date to be transferred to a computer for a series of data analysis; the concentration value of each marker in unknown samples is obtained according to the concentration value of each marker contained in each standard product, and the obtain value is output in a report form. The signal analysis system of the present invention realizes simultaneously reading and calculating signals of a plurality of biochips (each biochip has a plurality of signals of substances to be detected), which greatly saves data analysis time. The signal analysis system has the advantages of high reliability and stabilization and large application range, and not only can be applied to quantitative instruments during the clinical application of biochip reagent kits, but also can be combined with other biochips.

Description

The multiple-marknig-object biological chip signal analyzing method
Technical field:
The invention belongs to biomedicine field, be specifically related to a kind of signal analysis method of many marks biochip.
Background technology:
Biochip technology is that a kind of new bio that rises middle 1990s learns a skill.It is based on the large-scale parallel analytical approach of biomacromolecule (nucleic acid, protein etc.) interphase interaction, in conjunction with multi-field technology such as microelectronics, micromechanics, chemistry, physics, computing machines, with process serializations, integrated, microminiaturized such as example reaction related in the life science, detection, analyses, become one of current life science field technology with fastest developing speed.Major company of a few family such as PACKARD company, Hewlett-Packard Corporation, GENERAL SCANNING company and TELECHEN company etc. have been arranged at present in the world all in exploitation biochip detecting and analysing system, and made major contribution aspect some in point sample, chip detection, data acquisition and processing (DAP) etc.These equipment performances are good, simple to operation, but cost an arm and a leg.Domestic exploitation to this quasi-instrument still is in conceptual phase, thereby is necessary the performance of system is improved and improved.
Simultaneously, in Application of Biochips, particularly in the application of chip of expression spectrum, owing to be that expression at measured object changes and measures under a lot of situations, but not measure whether expressing, so need a kind of quantitative system of detection chip detection thing.And existing a lot of chip detecting system all is based on and detects whether expressing, and promptly detects qualitatively, and is not suitable for detection by quantitative.
CCD (charge-coupled image sensor) imageing sensor is made with a kind of semiconductor material of ISO, can change light signal into electric signal, converts digital signal to by the analog to digital converter chip again.Under the resolution of same maximum photographic images, the resolution of CCD is the bigger the better.Theoretically, all there is thermonoise in any amplifying circuit.Reduce thermonoise, the best approach that improves signal to noise ratio (S/N ratio) is the environment that sensitive film and amplifying circuit is placed low temperature.Usually use the method for fluorescence radiation in the chip research in the past, the brightness of image of its generation is low, contrast is low, is unfavorable for reading.Because a characteristic of biochip is the bio signal of trace, the absolute value of signal is very weak usually, and under these circumstances, the signal to noise ratio (S/N ratio) that the raising signal reads instrument is necessary.
Summary of the invention:
Technical matters to be solved by this invention is to pass through chemiluminescence method, adopt ccd image sensor, X-Y-Z-θ locating device and software systems, a kind of favorable reproducibility is provided, but the multiple-marknig-object biological chip signal analyzing systems of detection by quantitative, quantitative test liquid concentration to be measured.
Multiple-marknig-object biological chip signal analyzing systems disclosed by the invention is and the matching used analytic system of biological chips detection system that wherein biological chips detection system comprises a plurality of biochips, a plurality of standard items, quality-control product, reactant liquor, cleansing solution, detection liquid; Multiple-marknig-object biological chip signal analyzing systems comprises image capturing system, image processing system, data analysis and output system; Image capturing system comprises the X-Y-Z-θ locating device of CCD camera system and light sealing; Image processing system and data analysis output system are made of software, and image processing system can be realized background processing, adjustment contrast, amplify multinomial functions such as dwindling, rotate, fill (assorted some removal), histogram demonstration, the calibration of abnormal limit and Morphological; Data analysis and output system can realize the making of the signal-concentration standard curve of each mark on the biochip, the quantitative and report output of each mark concentration in the specimen.
Signal Analysis System of the present invention is by the quantitative test of following step realization to chip detecting system:
1) each component of chip detecting system is reacted: unknown sample, each standard items and quality-control product (solution or dried frozen aquatic products redissolution liquid) are all added biochip react with it, add reactant liquor after the washing more respectively and react.Detect liquid join with the reacted biochip of reactant liquor in, make the ad-hoc location on the chip produce luminous signal.
2) take the light signal on a plurality of biochips simultaneously by the refrigeration type CCD (cool CCD) in the Signal Analysis System, and be translated into view data, transfer to computing machine and signal is carried out a series of data analyses, try to achieve the concentration value of each mark in the unknown sample according to the concentration value of contained each mark in each standard items, and with the form output of the value of trying to achieve with form.
At the more weak characteristics of chip light signal, used CCD is refrigeration type (cool CCD) in the CCD camera system of the present invention.Cool CCD compares with normal CCD in low-temperature condition (being lower than 0 ℃) operate as normal, and the picture noise that cool CCD takes is low, thus resolution and highly sensitive, and signal to noise ratio (S/N ratio) is better.
In the common image processing system, when CCD takes, be used with the X-Y-Z 3 D locating device, X-Y plane is regulated the horizontal level of measured object, and the Z direction is regulated the distance of object and camera lens.And in the present invention, use X-Y-Z-θ locating device first, the implication of X-Y and Z is constant, but has increased the regulatory function of on surface level the angle of object being rotated.Because the biochip Signal Analysis System is taken when being used for a large amount of signal and is analyzed, so if change to some extent, can making, each signal position analyzes the difficulty that becomes, can cause the mistake of data when serious.
θ locating device among the present invention is to simplify the back with the principle of worm and gear to form, and converts rectilinear motion a kind of structure of circular motion to, and angular adjustment is carried out in the orientation on the plane, can realize-30 spending+range of adjustment of 30 degree.
The software of data analysis carries out quantitative principle to unknown sample and is in the system of the present invention: by read to the biochip of each standard items reaction on signal value, set up the curve that concerns between the signal value on each mark concentration in the standard items and the corresponding biochip, calculate the concentration of unknown sample again by the corresponding signal value that reads unknown sample.
Below each several part function in the system of the present invention is further described:
1, image capturing system: chip detection is carried out the parameter setting, and take image.
2, image processing system: can realize background processing, adjustment contrast, amplify multinomial functions such as dwindling, rotate, fill (assorted some removal), histogram demonstration, the calibration of abnormal limit and Morphological.Following three functions of main realization:
1) selected image region is amplified;
2) increase visual contrast;
3) a little remove there being assorted some place to mix on the image.
3, data analysis and output system
1) makes typical curve
According to the concentration value of each mark in each standard items, corresponding signal value on biochip, make " signal-concentration " typical curve of each mark.
2) to each mark concentration in the unknown sample quantitatively
Adopt large form that a plurality of subarrays are carried out one-time positioning, adopt little template that the sample of each subarray is positioned again.Get the signal value of 4 the brightest in each sample signal pixel average gray, from image, obtain signal value, obtain concentration value by typical curve as each point.
3) report output
Form with form in Excel provides each mark Determination on content result in each unknown sample.
Be to realize above-mentioned functions, the software that check and analysis of the present invention system adopts is technology platform with VC.The specific implementation method is as follows:
1. obtain image
It is a definite value in 10 seconds to 5 minutes that system of the present invention is provided with the time shutter, is generally 15 seconds or 60 seconds.Implementation method is: be provided with from the time shutter shown in Figure 1 and import time shutter m_ExpTime the dialog box, pass to variable exposure_time, by function PICM_SetExposure (exposure_time , ﹠amp; Error) realize the time shutter.
System of the present invention is provided with the CCD temperature and is any one value of-10 ℃ to-50 ℃, is generally-20 ℃.Implementation method is: from temperature shown in Figure 2 the temperature setTmp that input is provided with the dialog box is set, controls the CCD temperature by function PICM_Set_Temperature (setTmp).
Under " obtaining instruction ", obtain chip image, be stored in the computing machine by camera system.(when buying CCD, software promptly possesses this function in the image collection card that producer provides.)
2. image processing
Under " image transform " instructs, mainly carry out instructions such as " amplification ", " contrast enhancing " on demand, adjust the visual size that shows, contrast etc., use the abnormity point in " filling " instruction removal chip image in case of necessity.Implementation method is as follows:
1) amplifies
Earlier with the selected image region that will amplify of mouse, calculate the width of the selected image of enlargement factor tx=subwindow width rectClient.right/ of x, y direction, the height of the selected image of ty=subwindow height rectClient.bottom/, zooming multiple m_Scale gets tx, smaller value among the ty;
Calculate the center Center1 before selection area amplifies, center after then amplifying is Center2=Center1*m_Scale, after zooming m_Scale times, the view scroll bar needs horizontal rolling Scrollpt.x=Center2.x-rectClient.right/2, vertical scrolling Scrollpt.y=Center2.y-rectClient.bottom/2.
2) adjust contrast
1. to regulate the zone of contrast with mouse is selected, the number n ValidPixel of pixel in the zoning, the gray-scale value of this nValidPixel pixel is placed among the nSort, with function heapsort (nSort, nValidPixel) by the gray-scale value size nSort is sorted, the gray-scale value of getting the 95%th pixel is as the upper limit, dSMax=nSort[(0.95*nValidPixel-1)], the gray-scale value of getting the 5%th pixel is as lower limit, dSMin=nSort[0.05*nValidPixel];
Gray-scale value mybits (value 0 ~ 255) when 2. computational picture shows, if visual original gray value data (0 ~ 4095) is greater than dSMax, mybits=255 then; If less than dSMin, mybits=0 then; Otherwise calculate the value of mybits by straight line shown in Figure 12, i.e. mybits=(int) (* data*dA+dB), dA=255.0/ (double) (dSMax-dSMin), dB=-dA*dSMin.
3) fill
Fill processing for assorted point, earlier with the selected assorted point of mouse zone, come for filling this zone with value SpotValue, the computing method of SpotValue are: outside selected assorted zone (3 pixel width), look for the pixel of gray-scale value between 40 ~ 150, the mean value of getting these pixels is as SpotValue, if the number of putting is 0, then SpotValue gets 80.
3. data analysis and output (working interface is seen Fig. 3)
1) makes typical curve
Implementation method is to set up the index dialog box.When relating to x index, analytic target (is respectively index 1, index 2, index x) time, the concentration value of the various indexs of input in dialog box, assignment is given variable m_ index 1 successively, m_ index 2, m_ index x, import each concentration gradient value, deposit array StandardC[x] in [n] (n refers to the quantity of concentration gradient), from image, read the signal value of each standard items again, method is: give each standard items array location with little template, regulate the array line number of this template, columns, line space, column pitch, template size, template position makes all grids of template behind the location just fix all signaling points of a biochip, and each lattice only contains 1 signaling point.Get in each lattice the brightest 4 pixel average gray as the signal value StandardPixAve[i of each point] [SD], simulate the typical curve of x kind mark respectively according to concentration value, signal value, the match mode is seen Figure 13, corresponding to each concentration gradient Ci, the signal value that simulates is designated as Huidu[i] [SD], can use different match modes to each tumor markers, as x=ay 2+ by+c, y=a 1g (x)+b, y=a+bx c/ (1+dx e) wait (wherein x is a concentration value, and y is that signal value or x are signal value, and y is a concentration value); Also can use the combination of multiple match mode.
2) to each tumor-marker substrate concentration in the unknown sample quantitatively
Both can analyze during this running software, also can analyze the signal of a plurality of unknown sample (corresponding to a plurality of biochips) to the signal of single unknown sample (corresponding to a biochip).Their implementation method is slightly different.
If once only handle single unknown sample: array location (this template array row, column of giving each unknown sample correspondence with little template, the size, the position is all adjustable), get in each lattice the brightest 4 pixel average gray as the signal value StandardPixAve[i of each point] [SD], according to the equation of aforementioned 2 typical curves of making, calculate the concentration value of each point.
If a plurality of unknown sample of disposable processing: suppose that sample number is 48, be arranged as 6*8 subarray.
(1) size of adjustment large form, its position simultaneously moves up and down, make each array of itself and image roughly overlapping, with the upper left corner coordinate position of 48 grids in this template ideal position LS_IdealPoint[i as each subarray] [j], then with little template to each subarray location.
(2) after the little Template Location, the locating information dialog box can appear, see Figure 11, click " location " button of dialog box, preserve the coordinate in this template upper left corner, as the real coordinate position LS_ActualPoint[i of this subarray] [j], calculate and search for the nearest LS_IdealPoint[i of this coordinate distance] [j], set it and be the array of this position (as the A1 subarray), hide the pairing button of this array, method is given each subarray location successively in view of the above.
(3) by the LS_ActualPoint[i that writes down] [j], one-time calculation goes out the signal value of each subarray, draws concentration value by signal value, sees 3. data analysis parts;
(4) concentration value of each each index of subarray is all exported in Excel, represented each subarray and its sample source with the position of each subarray.
The workflow of system of the present invention is seen Fig. 4.
Biochip Signal Analysis System favorable reproducibility of the present invention, reliable and stable, easy and simple to handle directly perceived, have very high practical value.Particularly this Signal Analysis System can read and calculate simultaneously to the signal of a plurality of biochips (signal that a plurality of measured matters are arranged on each biochip), has greatly saved the data-analysis time.Quantitative instrument when this analytic system not only can be used for the protein chip kit clinical practice also can be used in combination with other biochip.
Below in conjunction with embodiment check and analysis of the present invention system is further described.
Description of drawings:
Fig. 1. the time shutter is provided with dialog box
Fig. 2. temperature is provided with dialog box
Fig. 3. the working interface of software
Fig. 4. the software operation FB(flow block)
Fig. 5. the chip signal image was for example before contrast was adjusted
Fig. 6. the chip signal image is for example after the contrast adjustment
Fig. 7. a plurality of array large forms location is for example
Fig. 8. the little Template Location of each subarray is for example
Fig. 9. the typical curve of match is for example
Figure 10. the test results report with report form output is for example single
Figure 11. the locating information dialog box
Figure 12. contrast variation's curve
Figure 13. typical curve match flow process
Embodiment:
Be used to detect the biochip Signal Analysis System of 12 kinds of tumor-marker substrate concentrations.Sub computers be configured to PentiumIII 600 processors, 256 MB of memory, the 20G hard disk, 256 look SVGA, operating system is Windows98, application software is Office97 and biochip image analytic system software of the present invention.
Described system is as the support equipment of 48 person-portions " multi-tumor marker protein chip detection system ", can carry out quantitative measurement to 12 kinds of clinical tumor markers content commonly used such as AFP, PSA, free-PSA, HGH, β-hCG, CEA, NSE, CA19-9, CA242, CA15-3, CA125, Ferritin in the serum simultaneously, not only improved the diagnosis accuracy of planting tumour, and realized associating auxiliary diagnosis kinds of tumors to single.This system not only is applied to clinical detection to tumour, more is applicable to the cancer screening to asymptomatic crowd.
1, obtains image
It is 60 seconds that time shutter is set, and implementation method is: be provided with from the time shutter shown in Figure 1 and import time shutter m_ExpTime the dialog box, pass to variable exposure_time, by function PICM_SetExposure (exposure_time , ﹠amp; Error) realize the time shutter.
The CCD temperature is set is-20 ℃, implementation method is: from temperature shown in Figure 2 the temperature setTmp that input is provided with the dialog box is set, controls the CCD temperature by function PICM_Set_Temperature (setTmp).
Under " obtaining instruction ", obtain chip image, be stored in the computing machine by camera system.
2, image processing
Under " image transform " instructs, mainly carry out instructions such as " amplification ", " contrast enhancing " on demand, adjust the visual size that shows, contrast etc., use the abnormity point in " filling " instruction removal chip image in case of necessity.Implementation method is as follows:
1) amplifies
Earlier with the selected image region that will amplify of mouse, calculate the width of the selected image of enlargement factor tx=subwindow width rectClient.right/ of x, y direction, the height of the selected image of ty=subwindow height rectClient.bottom/, zooming multiple m_Scale gets tx, smaller value among the ty;
Calculate the center Center1 before selection area amplifies, center after then amplifying is Center2=Center1*m_Scale, after zooming m_Scale times, the view scroll bar needs horizontal rolling Scrollpt.x=Center2.x-rectClient.right/2, vertical scrolling Scrollpt.y=Center2.y-rectClient.bottom/2.
2) adjust contrast
1. to regulate the zone of contrast with mouse is selected, the number n ValidPixel of pixel in the zoning, the gray-scale value of this nValidPixel pixel is placed among the nSort, with function heapsort (nSort, nValidPixel) by the gray-scale value size nSort is sorted, the gray-scale value of getting the 95%th pixel is as the upper limit, dSMax=nSort[(0.95*nValidPixel-1)], the gray-scale value of getting the 5%th pixel is as lower limit, dSMin=nSort[0.05*nValidPixel];
Gray-scale value mybits (value 0 ~ 255) when 2. computational picture shows, if visual original gray value data (0 ~ 4095) is greater than dSMax, mybits=255 then; If less than dSMin, mybits=0 then; Otherwise calculate the value of mybits by straight line shown in Figure 12, i.e. mybits=(int) (* data*dA+dB), dA=255.0/ (double) (dSMax-dSMin), dB=-dA*dSMin.
3) fill
Fill processing for assorted point, earlier with the selected assorted point of mouse zone, come for filling this zone with value SpotValue, the computing method of SpotValue are: outside selected assorted zone (3 pixel width), look for the pixel of gray-scale value between 40-150, the mean value of getting these pixels is as SpotValue, if the number of putting is 0, then SpotValue gets 80.
Fig. 5 for contrast adjust before the chip signal image for example, Fig. 6 be that the chip signal image is given an example after the contrast adjustment.
3, data analysis and output (working interface is seen Fig. 3)
1) makes typical curve
Implementation method is to set up the index dialog box.When relating to x index, analytic target (is respectively index 1, index 2, index x) time, the concentration value of the various indexs of input in dialog box, assignment is given variable m_ index 1 successively, m_ index 2, m_ index x, import each concentration gradient value, deposit array StandardC[x] in [n] (n refers to the quantity of concentration gradient), from image, read the signal value of each standard items again, method is: give each standard items array location with little template, regulate the array line number of this template, columns, line space, column pitch, template size, template position makes all grids of template behind the location just fix all signaling points of a biochip, and each lattice only contains 1 signaling point.Get in each lattice the brightest 4 pixel average gray as the signal value StandardPixAve[i of each point] [SD], simulate the typical curve of x kind mark respectively according to concentration value, signal value, the match mode is seen Figure 13, corresponding to each concentration gradient Ci, the signal value that simulates is designated as Huidu[i] [SD], can use different match modes to each tumor markers, as x=ay 2+ by+c, y=a 1g (x)+b, y=a+bx c/ (1+dx e) wait (wherein x is a concentration value, and y is that signal value or x are signal value, and y is a concentration value); Also can use the combination of multiple match mode.
2) to each tumor-marker substrate concentration in the unknown sample quantitatively
Sample number is 48, is arranged as 6*8 subarray.
(1) size of adjustment large form, its position simultaneously moves up and down, make each array of itself and image roughly overlapping, with the upper left corner coordinate position of 48 grids in this template ideal position LS_IdealPoint[i as each subarray] [j], then with little template to each subarray location.
(2) after the little Template Location, the locating information dialog box can appear, see Figure 11, click " location " button of dialog box, preserve the coordinate in this template upper left corner, as the real coordinate position LS_ActualPoint[i of this subarray] [j], calculate and search for the nearest LS_IdealPoint[i of this coordinate distance] [j], set it and be the array of this position (as the A1 subarray), hide the pairing button of this array, method is given each subarray location successively in view of the above.
(3) by the LS_ActualPoint[i that writes down] [j], one-time calculation goes out the signal value of each subarray, draws concentration value by signal value, sees 3. data analysis parts;
(4) concentration value of each each index of subarray is all exported in Excel, represented each subarray and its sample source with the position of each subarray.The 6*8 array is located simultaneously, see the big array location of Fig. 7 .6*8; To the signal framing of each subarray, see Fig. 8. signal is arranged as the subarray location of 5*5; Make typical curve, see Fig. 9. with the CA125 typical curve of quadratic equation match; Calculate 12 tumor markers concentration, data outputs separately in the unknown sample, see Figure 10. show with 12 tumor-marker substrate concentrations in the sample of the chip reaction of A1 position.

Claims (4)

1. a multiple-marknig-object biological chip signal analyzing method is characterized in that this method comprises the following steps:
(1) image capturing system carries out parameters C CD temperature, time shutter setting to chip detection, carries out picture-taking then; Wherein image capturing system comprises the X-Y-Z-θ locating device of CCD camera system and light sealing; The CCD camera system is the refrigeration type, and temperature range is-50 ℃ to-10 ℃; X-Y-Z represents three-dimensional localization in the X-Y-Z-θ locating device, and θ is illustrated on the surface level and spends+the 30 rotations adjusting location of spending from-30;
(2) image processing system amplifies, increases contrast and assorted some removal with selected image region;
(3) data analysis and report output:
1) makes typical curve
According to the concentration value of each mark in each standard items, corresponding signal value on biochip, make the signal-concentration standard curve of each mark;
2) to each mark concentration in the unknown sample quantitatively
Adopt large form that a plurality of subarrays are carried out one-time positioning, adopt little template that the sample of each subarray is positioned again, get the signal value of 4 the brightest in each sample signal pixel average gray, from image, obtain signal value, obtain concentration value by typical curve as each point;
3) report output.
2. a multiple-marknig-object biological chip signal analyzing method as claimed in claim 1 is characterized in that the CCD temperature that wherein said image capturing system is provided with is-20 ℃.
3. multiple-marknig-object biological chip signal analyzing method as claimed in claim 1, the time shutter scope that it is characterized in that wherein said image capturing system setting is 10 seconds to 5 minutes.
4. multiple-marknig-object biological chip signal analyzing method as claimed in claim 3, the time shutter that it is characterized in that wherein said image capturing system setting is 60 seconds.
CNB021363706A 2002-08-02 2002-08-02 Multiple-marknig-object biological chip signal analyzing systems Expired - Fee Related CN1255671C (en)

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PCT/CN2003/000123 WO2004013627A1 (en) 2002-08-02 2003-02-08 System and method for analyzing signals in a multi-markers protein chip
AU2003211848A AU2003211848A1 (en) 2002-08-02 2003-02-08 System and method for analyzing signals in a multi-markers protein chip

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