Signal processing method in autoradiography

• US 4,837,733 A
• Filed: 07/10/1986
• Issued: 06/06/1989
• Est. Priority Date: 01/08/1983
• Status: Expired due to Term

• Current Assignee: Fuji Photo Film Co Limited (Fujifilm Holdings Corporation)
• Original Assignee: Fuji Photo Film Co Limited (Fujifilm Holdings Corporation)
• Inventors: Kimura, Tsutomu, Hishinuma, Kazuhiro, Shiraishi, Hisashi
• Primary Examiner(s): Atkinson, Charles E.
• Assistant Examiner(s): Meyer, Charles B.
• Application Number:
  US06/883,922
• Time in Patent Office: 1,062 Days
• Field of Search: 204/180 R, 204/180 P, 204/180 G, 204/299 R, 250/458.1, 250/459.1, 250/461.1, 250/374, 250/375, 250/388, 435/35, 435/802, 435/803, 435/6, 436/169, 436/174, 364/413, 364/414
• US Class Current: 250/583
• CPC Class Codes: G01T 1/2012 using stimulable phosphors, e.g. stimulable phosphor sheets
• CPC Class Codes: G01T 1/2014 Reading out of stimulable sheets, e.g. latent image

Abstract

A signal processing method in autoradiography for obtaining information on the one dimensional location of radioactively labeled substances in a sample where the substances of the sample are distributed in at least one row on a support medium where the information is in the form of symbols, numerals or a combination thereof. The method at least includes the steps of (1) generating digital image data where the data comprises sets of digital signals corresponding to the autoradiograph including the row of distributed substances and where the sets of digital signals may respectively represent successive linear portions of the autoradiograph; (2) scanning selected digital signals of the digital image data to generate at least one further signal representative of a predetermined portion of the row of distributed substances where the position of the predetermined portion is at least partially determined by its location in the scanning direction and the amount of radioactively labeled substance at the location is at least partially determined by the amplitude of the further signal; (3) processing the further signal with either or both of smoothing and threshold-processing to detect sampling point corresponding to the location of the predetermined portion of the row of distributed substances; (4) obtaining the image data digital corresponding to the autoradiograph having the locational information on the radioactively labeled substances where the digital image data is obtained by utilizing a radiation image recording and reproducing method of employing a stimulable phosphor sheet. A signal processing method for determining the base sequence of DNA is also disclosed.

Claims

1. A signal processing method for processing an autoradiograph recorded on a support medium and containing locational information on the one dimensional location of radioactively labeled substances in a sample where the substances are distributed in at least one one dimensional direction on said support medium to form at least one row of the distributed substances,

which comprises the steps of:

(1) generating digital image data where the data comprises sets of digital signals corresponding to the autoradiograph including the row of distributed substances;

(2) scanning said digital image data in at least two different positions in such a manner that each scanning selects certain ones of said digital signals corresponding to the row of distributed substances to obtain relationships between positions of said certain ones of the digital signals in the direction of the scanning and the signal levels at said positions;

(3) generating at least two distributed point signals based on said relationships where the two distributed point signals are generated for said row of distributed substances, the two distributed point signals respectively corresponding to the two different scanning positions and where said two distributed points are disposed on said row;

(4) generating a signal corresponding to a continuous line selected from the group consisting of a straight line, a curved line and a polygonal line connecting said points on the row where said continuous line corresponds to a scanning line for detection of sampling points respectively corresponding to the locations of said substances;

(5) scanning said digital image data along said scanning line to obtain locational information signals representative of said locational information for each of said substances in said sample;

(6) said digital image data being generated by (a) causing a stimulable phosphor sheet to absorb radiation energy emitted by the radioactively labeled substances on the support medium to record the autoradiograph of the radioactively labeled substances on the stimulable phosphor sheet, (b) scanning said stimulable phosphor sheet with an electromagnetic wave to release as stimulated emission at least a portion of the radiation energy absorbed by said phosphor sheet in the form of the autoradiograph, (c) detecting said stimulated emission photoelectrically, and (d) converting the detected stimulated emission into said digital image data; and

whereby said locational information signals can be obtained in spite of one or more deviations of said row of said distributed substances from a straight line due to the compensation effected by said scanning line for said deviations where said deviations may be present in the support medium and/or the stimulable phosphor sheet.

2. The signal processing method in autoradiography as claimed in claim 1, wherein the scanning of the digital image data in at least two different positions is carried out in parallel.

3. The signal processing method in autoradiography as claimed in claim 1 or 2, wherein the width of said scanning on the digital image data is set prior to the signal processing where the number of said selected certain ones of the digital signals is so chosen as to be at least equal to the number of digital signals corresponding to one of said radioactively labeled substances to thus set the width of the scanning.

4. The signal processing method in autoradiography as claimed in claim 1 or 2, where said continuous line is a straight line.

5. The signal processing method in autoradiography as claimed in claim 1 or 2, wherein said radioactively labeled substances arranged to form a row of distributed substances on the support medium are biopolymers, derivatives thereof, or cleavage products of either said biopolymers or said derivatives thereof, labeled with a radioactive element and resolved in said one dimensional direction on the support medium.

6. The signal processing method in autoradiography as claimed in claim 5, wherein said biopolymers are nucleic acids, derivatives thereof or cleavage products of either said nucleic or said derivatives thereof.

31. The signal processing method as in claims 1, 7, 13, 16, 19, 21, 23, 25 or 27, wherein said digital image data is stored in a memory

7. A signal processing method for processing an autoradiograph recorded on a support medium and containing locational information on the one dimensional location of radioactively labeled substances in a sample where the substances are distributed in at least one one dimensional direction on said support medium to form at least one row of the distributed substances, and locational informational signals in the form of symbols, numerals, or a combination thereof are obtained regarding said locational information,

which comprises a process including:

(1) generating digital image data where the data comprises sets of digital signals corresponding to the autoradiograph including the row of distributed substances;

(2) scanning selected digital signals of said digital image data to generate at least one further signal representative of a predetermined portion of said one row of distributed substances where the position of said portion is at least partially determined by its location in the scanning direction and the amount of said radioactively labeled substance at said location is at least partially determined by the amplitude of said further signal;

(3) processing said further signal to detect at least one sampling point correspond to the location of said predetermined portion of said one row of distributed substances;

(4) processing said digital image data, in response to said processed further signal, to obtain at least one of said locational informational signals representative of said locational information for at least one of said substances in said sample;

(5) said digital image data being generated by (a) causing a stimulable phosphor sheet to absorb radiation energy emitted by said radioactively labeled substances on the support medium to record the autoradiograph of the radioactively labeled substances on the stimulable phosphor sheet, (b) scanning said stimulable phosphor sheet with an electromagnetic wave to release as stimulated emission at least a portion of radiation energy stored in said phosphor sheet in the form of the autoradiograph, (c) detecting said stimulated emission photoelectrically and (d) converting the detected stimulated emission into said digital image data.

8. The signal processing method in autoradiography as claimed in claim 7, wherein said smoothing is performed by convolution of the further signal with a filter function.

9. The signal processing method in autoradiography as claimed in claim 7 or 8, wherein the location of the maximum value of the smoothed, further signal corresponds to said sampling point.

10. The signal processing method in autoradiography as claimed in claim 7 or 8, wherein the middle point of said processed, further signal corresponds to said sampling point.

11. The signal processing method in autoradiography as claimed in claim 10, wherein the threshold value for said threshold-processing is determined based on a histogram.

12. The signal processing method in autoradiography as claimed in claim 7 or 8, wherein said radioactively labeled substances distributed on the support medium are biopolymers, derivatives thereof, or cleavage products of either said biopolymers or said derivatives thereof, labeled with a radioactive element.

13. A signal processing method for processing an autoradiograph recorded on a support medium and containing the locational information on the one dimensional location of groups of radioactively labeled substances in a sample where the substances are arranged in plural rows including a reference row where each row is distributed in at least one one dimensional direction on said support medium, and locational informational signals in the form of symbols, numerals or a combination thereof are obtained regarding said locational information,

which comprises a process including:

(1) generating digital image data where the data comprises sets of digital signals corresponding to the autoradiograph including the rows of distributed substances;

(2) scanning selected digital signals of said digital image data to generate further signals representative of predetermined portions of said rows of distributed substances where the positions of said portions are at least partially determined by their location in the scanning direction and the amounts of said radioactivity labeled substances at said locations are at least partially determined by the amplitudes of said further signals;

(3) processing said further signals to detect candidate sampling points corresponding to possible locations of certain ones of said substances in each of said rows;

(4) processing said candidate sampling points statistically to determine fundamental sampling points respectively corresponding to actual locations of said certain ones of said substances;

(5) detecting the remaining sampling points in each of said rows based on said fundamental sampling points to obtain said locational informational signals representative of said locational information for the remaining ones of said substances in each of said rows in said sample; and

(6) said digital image data being generated by (a) causing a stimulable phosphor sheet to absorb radiation energy emitted by said groups of radioactively labeled substances on the support medium to record the autoradiograph of the groups of radioactively labeled substances on the stimulable phosphor sheet, (b) scanning said stimulable phosphor sheet with an electromagnetic wave to release as stimulated emission at least a portion of radiation energy stored in said phosphor sheet in the form of the autoradiograph, (c) detecting said stimulated emission photoelectrically and converting the detected stimulated emission into said digital image data.

14. The signal processing method in autoradiography as claimed in claim 13, wherein said radioactively labeled substances distributed on the support medium are biopolymers, derivatives thereof, or cleavage products of either said biopolymers or said derivatives thereof, labeled with a radioactive element.

15. The signal processing method in autoradiography as claimed in claim 14, wherein said biopolymers are nucleic acids, derivatives thereof or cleavage of either said nucleic acids or said derivatives products thereof;

and said symbols, numerals or a combination thereof;

obtained by said signal processing method represents a base sequence of said biopolymers.

32. The signal processing method of claims 7, 13, 16, 19 or 21 where said processing of the further signal includes subjecting the further signal to threshold processing.

33. The signal processing method of claim 32 where said signal processing includes smoothing the further signal.

16. A signal processing method for processing an autoradiograph recorded on a support medium and containing locational information on the one dimensional location of groups of radioactively labeled substances in a sample where the substances are arranged in plural rows where each row is distributed in at least one one dimensional direction on said support medium, and locational informational signals in the form of symbols, numerals or a combination thereof are obtained regarding said locational information,

which comprises a process including:

(1) generating digital image data where the data comprises sets of digital signals corresponding to the autoradiograph including the rows of distributed substances;

(2) synthesizing a reference row from said plural rows of distributed substances,

(3) scanning selected digital signals of said digital image data to generate further signals representative of predetermined portions of said rows of distributed substances where the positions of said portions are at least partially determined by their locations in the scanning direction and the amounts of said radioactively labeled substances at said locations are at least partially determined by the amplitude of said further signals;

(4) processing said further signals to detect candidate sampling points corresponding to possible locations of certain ones of said substances in each of said rows;

(5) processing said candidate sampling points statistically to determine fundamental sampling points respectively corresponding to actual locations of said certain ones of said substances; and

(6) detecting the remaining sampling points in each of said rows based on said fundamental sampling points to obtain said locational informational signals representative of said locational information for the remaining ones of said substances in each of said rows in said sample;

said digital image data being generated by (a) causing a stimulable phosphor sheet to absorb radiation energy emitted by said groups of radioactively labeled substances on the support medium to record the autoradiograph of the groups of radioactively labeled substances on the stimulable phosphor sheet, (b) scanning said stimulable phosphor sheet with an electromagnetic wave to release as stimulated emission at least a portion of radiation energy stored in said phosphor sheet in the form of the autoradiograph, (c) detecting said stimulated emission photoelectrically and (d) converting the detected stimulated emission into said digital image data.

17. The signal processing method in autoradiography as claimed in claim 16, wherein aid radioactively labeled substances distributed on the support medium are biopolymers, derivatives thereof, or cleavage products of either said biopolymers or said derivatives thereof, and said symbols, numerals, or a combination thereof obtained by said signal processing method represents a base sequence of said biopolymers.

18. The signal processing method in autoradiography as claimed in claim 17, wherein said biopolymers are nucleic acids, derivatives thereof or cleavage products thereof, and said symbol, numeral or combination thereof obtained by said signal processing represents base sequence thereof.

19. A signal processing method for processing an autoradiograph recorded on a support medium and containing a base sequence of DNA or a DNA fragment, employing at least five groups of base specific cleavage products comprisng:

(1) a mixture of guanine specific cleavage products, adenine specific cleavage products, thymine specific cleavage products and cytosine specific cleavage products;

(2) guanine specific cleavage products;

(3) a mixture of guanine specific cleavage products and adenine specific cleavage products;

(4) a mixture of thymine specific cleavage products and cytosine specific cleavage products; and

(5) cytosine specific cleavage products,

which are obtained by specific cleavage of the DNA or DNA fragment which has been labeled with a radioactive element where each of said groups is resolved in at least one one dimensional direction so that said groups are in substantial parallel relation to each other to form resolved rows on the support medium,

said signal processing method including the steps of;

(1) generating digital image data where the data comprises sets of digital signals corresponding to the autoradiograph including the row of cleavage products;

(2) utilizing an internal reference row comprising the resolved row of said mixture (1) of base specific cleavage products;

(3) scanning selected digital signals of said digital image data to generate further signals representative of predetermined portions of said rows of cleavage products where the positions of said portions are at least partially determined by their locations in the scanning direction and the amounts of said radioactively labeled cleavage products at said locations are at least partially determined by the amplitudes of said further signals;

(4) processing said further signals to detect candidate sampling points corresponding to possible locations of certain ones of said cleavage products in each of said rows;

(5) processing said candidate sampling points statistically to determine fundamental sampling points respectively corresponding to actual locations of said certain ones of said cleavage products;

(6) detecting the remaining sampling points in each of said resolved rows based on said fundamental sampling points to obtain signals representative of the locations of the remaining cleavage products in said sample; and

(7) comparing and identifying the positions of said sampling points in each of the resolved rows to obtain locational information on said guanine, adenine, thymine and cytosine,

(8) said digital image data being generated by (a) causing a stimulable phosphor sheet to absorb radiation energy emitted by said groups of radioactively labeled cleavage products on the support medium to record the autoradiograph of the groups of radioactively labeled cleavage products on the stimulable phosphor sheet, (b) scanning said stimulable phosphor sheet with an electromagnetic wave to release as stimulated emission at least a portion of radiation energy stored in said phosphor sheet in the form of the autoradiograph, (c) detecting said stimulated emission photoelectrically and (d) converting the detected stimulated emission into said digital image data.

20. The signal processing method in autoradiography as claimed in claim 19, wherein said statistical processing of the candidate sampling points to determine the fundamental sampling points comprises the steps of:

(1) approximating said candidate sampling points with the following equation (1);

space="preserve" listing-type="equation">W.sub.On =a-b log (A+M.sub.n) (1)

wherein W_On represents the distance between one of the candidate sampling points on one of the resolved rows and the starting point of the resolved row, n represents the number of the sampling point corresponding to said one candidate point, and A and M are constant values, where a and b are calculated by substituting values of W_On and n into Equation (1) to solve at least two equations with two unknowns--namely a and b; and

(2) determining the fundamental sampling points using the equation (1) with the calculated values of a and b.

21. A signal processing method for processing an autoradiograph recorded on a support medium and containing a base sequence of DNA or a DNA fragment, employing at least four groups of base specific cleavage products consisting of:

(1) guanine specific cleavage products;

(2) a mixture of guanine specific cleavage products and adenine specific cleavage products;

(3) a mixture of thymine specific cleavage products; and

(4) cytosine specific cleavage products,

which are obtained by specific cleavage of the DNA or DNA fragment which has been labeled with a radioactive element where each of said groups is resolved in at least one one dimentional direction so that said groups are in substantial parallel relation to each other to form resolved rows on the support medium,

said signal processing method including the steps of;

(1) generating digital image data where the data comprises sets of digital signals corresponding to the autoradiograph including the rows of cleavage products;

(2) synthesizing an internal reference row from the resolved rows;

(3) scanning selected digital signals of said digital image data to generate further signals representative of predetermined portions of said rows of cleavage products where the positions of said portions are at least partially determined by their locations in the scanning direction and the amounts of said radioactively labeled cleavage products at said locations are at least partially determined by the amplitudes of said further signals;

(4) processing said further signals to detect candidate sampling points corresponding to possible locations of certain ones of said cleavage products in each of said rows;

(5) processing said candidate sampling points statistically to determine fundamental sampling points respectively corresponding to actual locations of said certain ones of said cleavage products;

(6) detecting the remaining sampling points in each of the resolved rows based on said fundamental sampling points to obtain signals representative of the locations of the remaining cleavage products in said sample;

(7) comparing and identifying the positions of said sampling points on the resolved rows to obtain locational information on said guanine, adenine, thymine and cytosine,

(8) said digital image data being generated by (a) causing a stimulable phosphor sheet to absorb radiation energy emitted by said groups of radioactively labeled cleavage products on the support medium to record the autoradiograph of the groups of radioactively labeled cleavage products on the stimulable phosphor sheet, (b) scanning said stimulable phosphor sheet with an electromagnetic wave to release as stimulated emission at least a portion of radiation energy stored in said phosphor sheet in the form of the autoradiograph, (c) detecting said stimulated emission photoelectrically and (d) converting the detected stimulated emission into said digital image data.

22. The signal processing method in autoradiography as claimed in claim 21, wherein said statistical processing for the candidate sampling points to determine the fundamental sampling points comprises the steps of:

(1) approximating each candidate sampling point with the following equation (1);

space="preserve" listing-type="equation">W.sub.On =a-b log (A+M.sub.n) (1)

wherein W_On represents the distance between one of the candidate sampling points on one of the resolved rows and the starting point of the resolved row, n represents the number of the sampling point corresponding to said one condidate point, and A and M are constant values, where a and b are calculated by substituting values of W_On and n into Equation (1) to solve at least two equations with two unknowns--namely a and b; and

(1) determining the fundamental sampling points using the equation (1) with the calculated values of a and b.

23. A signal processing method for processing an autoradiograph recorded on a support medium and containing base sequence of DNA or a DNA fragment, employing at least four groups of base specific cleavage products respectively consisting of:

(1) guanine specific cleavage products;

(2) adenine specific cleavage products;

(3) thymine specific cleavage products; and

(4) cytosine specific cleavage products,

which are obtained by specific cleavage of the DNA or DNA fragment which has been labeled with a radioactive element where each of said groups is resolved in at least one one dimensional direction so that said groups are in substantial parallel relation to each other to form at least four resolved rows on a support medium,

said signal processing method including the steps of;

(1) generating digital image data where the data comprises sets of digital signals corresponding to the autoradiograph including the row of distributed substances;

(2) synthesizing a signal representative of an internal reference row from the digital image data representing said resolved rows where said internal reference row includes candidate sampling points for all four groups of said base specific cleavage products and determining fundamental sampling points respectively corresponding to said candidate sampling points with respect to said internal reference row; and

(3) analyzing the digital signals representative of the radioactively labeled cleavage products present within a sampling mask corresponding to a predetermined area and movable along each of said four resolved rows to positions respectively corresponding to the positions of the fundamental sampling points on the internal reference row to detect sampling points in each resolved row by utilizing the exclusiveness of the sampling points corresponding to each group in each row;

(4) said digital image data being obtained by (a) causing a stimulable phosphor sheet to absorb radiation energy emitted by said groups of radioactively labeled cleavage products on the support medium to record the autoradiograph of the groups of radioactively labeled cleavage products on the stimulable phosphor sheet, (b) scanning said stimulable phosphor sheet with an electromagnetic wave to release as stimulated emission at least a portion of the radiation energy stored in said phosphor sheet in the form of the autoradiograph, (c) detecting said stimulated emission photoelectrically, and (d) converting the detected stimulated emission into said digital image data.

24. The signal processing method in autoradiography as claimed in claim 23, wherein said fundamental sampling points in each resolved rows are detected by subjecting the digital signals to smoothing, threshold-processing and statistical processing.

25. A signal processing method for processing an autoradiograph recorded on a support medium and containing a base sequence of DNA or a DNA fragment, employing at least four groups of base specific cleavage products respectively consisting of:

(1) guanine specific cleavage products;

(2) adenine specific cleavage products;

(3) thymine specific cleavage products; and

(4) cytosine specific cleavage products,

which are obtained by specific cleavage of the DNA or DNA fragment which has been labeled with a radioactive element where each of said groups is resolved in at least one one dimensional direction so that said groupd are in substantial parallel relation to each other to form at least four resolved rows on a support medium,

said signal processing method including the steps of;

(1) generating digital image data where the data comprises sets of digital signals corresponding to the autoradiograph including the row of distributed substances;

(2) determining fundamental sampling points with respect to an internal reference row, said internal reference row comprising the resolved row of said mixture (5) of base specific cleavage products; and

(3) analyzing the digital signals representative of the radioactively labeled cleavage products present within a sampling mask corresponding to a predetermined area and movable along at least certain ones of said resolved rows to positions respectively corresponding to the positions of the fundamental sampling points on the internal reference row to detect sampling points in each resolved row by utilizing the exclusiveness of the sampling points corresponding to each group in each row;

(4) said digital image data being obtained by (a) causing a stimulable phosphor sheet to absorb radiation energy emitted by said groups of radioactively labeled cleavage products on the support medium to record the autoradiograph of the groups of radioactively labeled cleavage products on the stimulable phosphor sheet, (b) scanning said stimulable phosphor sheet with an electromagnetic wave to release as stimulated emission at least a portion of the radiation energy stored in said phosphor sheet in the form of the autoradiograph, (c) detecting said stimulated emission photoelectrically, and (d) converting the detected stimulated emission into said digital image data.

26. The signal processing method in autoradiography as claimed in claim 25, wherein said fundamental sampling points in each resolved rows are detected by subjecting the digital signals to smoothing, threshold-processing and statistical processing.

27. A signal processing method for processing an autoradiograph recorded on a support medium and containing that base sequence of DNA or a DNA fragment, employing at least two groups of base specific cleavage products respectively comprising:

(1) single base specific cleavage products or a mixture of two or three kinds of base specific cleavage products selected from the group consisting of guanine specific cleavage products, adenine specific cleavage products, thymine specific cleavage products and cytosine specific cleavage products; and

(2) a mixture of two, three or four kinds of base specific cleavage products containing at least one kind of the base specific cleavage products included in the above group (1),

which are obtained by specific cleavage of the DNA or DNA fragment which has been labeled with a radioactive element where each of said groups is resolved in at least one one dimensional direction so that said groups are in substantial parallel relation to each other to form at least two resolved rows respectively containing groups (1) and (2) on a support medium,

said signal processing method including the steps of;

(1) generating digital image data where the data comprises sets of digital signals corresponding to the autoradiograph including the row of distributed substances;

(2) operating on the digital signals representing the resolved row of the above group (1) and the resolved row of the above group (2) with respect to the corresponding positions on each resolved row to obtain a mathematically constructed resolved row; and

(3) determining sampling points with respect to said constructed resolved row;

(4) said digital image data being obtained by (a) causing a stimulable phosphor sheet to absorb radiation energy emitted by said groups of radioactively labeled cleavage products on the support medium to record the autoradiograph of the groups of radioactively labeled cleavage products on the stimulable phosphor sheet, (b) scanning said stimulable phosphor sheet with an electromagnetic wave to release as stimulated emission at least a portion of the radiation energy stored in said phosphor sheet in the form of the autoradiograph, (c) detecting said stimulated emission photoelectrically and (d) converting the detected stimulated emission into said digital image data.

28. The signal processsing method in autoradiography as claimed in claim 27, wherein said sampling points are determined by subjecting the digital signals corresponding to each said constructed resolved row to smoothing and/or threshold-processing.

29. The signal processing method in autoradiography as claimed in claim 27 or 28, wherein said group (2) consists essentially of a combination of the base specific cleavage products of said group (1) and another kind of base specific cleavage product, and said operation in step (2) is performed by subtraction.

30. The signal processing method in autoradiography as claimed in claim 29, wherein the combination of said group (1) and said group (2) is selected from the combinations consisting of

(A):

(1) guanine specific cleavage products; and

(2) a mixture of guanine specific cleavage products and adenine specific cleavage products,

(B)

(1) cytosine specific cleavage products; and

(2) a mixture of thymine specific cleavage products; and

cytosine specific cleavage products or

(C) a mixture of combinations (A) and (B).