JP4979516B2 - Image reading method and apparatus - Google Patents

Description

  The present invention relates to an image reading method and apparatus, and more specifically, a capillary in which through holes containing different types of probes are arranged in a predetermined pattern, and a specimen to which a fluorescent material is applied is selectively bonded to the probe. The present invention relates to an image reading method and apparatus for reading a fluorescent image from an array sheet.

  As a method for examining the function of a gene whose sequence has been clarified, an analysis method using base sequence information is known. In this analysis method, a biochip in which tens to tens of thousands of different kinds of gene peptides, proteins, antibodies and other biologically related substances are immobilized as probes is used.

  In a biochip, a gene whose sequence has been clarified or a sample such as a protein made based on the sequence of that gene is selectively bound to a probe immobilized on the biochip using a specific reaction. Thus, the biological function expression relationship between the specimen and the probe can be specified, and the function of the specimen such as a gene whose sequence has been clarified or a protein made based on the sequence of the gene can be known.

  The above analysis method will be specifically described by taking as an example the case where a capillary array sheet is used as a biochip. The capillary array sheet has a plurality of through-holes, and biological substances (probes) such as different types of gene peptides, proteins, and antibodies are fixed to the plurality of through-holes at a predetermined position by a gel. It is a biochip.

  In the analysis, firstly, a gene whose sequence has been clarified, or a sample such as a protein made based on the sequence of the gene is labeled with a fluorescent substance, and the sample labeled with this fluorescent substance is subjected to hybridization or the like. It selectively binds to a biological substance immobilized as a probe on the biochip.

  Next, by detecting the fluorescence from the fluorescent substance labeling the specimen as a fluorescent image using a fluorescence measuring device such as a fluorescent laser scanner or a fluorescent microscope, the specimen labeled with the fluorescent substance is bound to which probe. As a result, it is possible to identify the biological function expression relationship between the sample such as a gene whose sequence has been clarified and the probe, and to know the function of the sample such as the gene whose sequence has been clarified.

  In the analysis using such fluorescent images, if there is a foreign substance in the through-hole of the capillary array sheet, the fluorescence from the foreign substance is detected as a bright spot, and the fluorescence from the fluorescent substance to be detected is accurately detected. There was a problem that was disturbed.

In order to solve such problems, multiple spots with the same type of probe immobilized are prepared and based on emission intensity excluding abnormally high emission intensity (for example, 1.5 times the lowest emission intensity or more) A processing method for obtaining a reading value is known (see Patent Document 1).
There is also known a method of identifying the position of a foreign substance by irradiating light having a wavelength that excites only the foreign substance, and excluding data of this part (see Patent Document 2).

JP 2004-101376 A Japanese Patent No. 3576523

  However, in the method of obtaining the reading value based on the emission intensity excluding the abnormally high emission intensity, it is necessary to prepare a plurality of spots to which the same type of probe is fixed, which increases the cost.

  In addition, in the method of identifying a foreign substance by irradiating light with a wavelength that excites only the foreign substance and excluding the foreign substance data, when the fluorescent substance that labels the sample is excited with light having the same wavelength as the foreign substance, that is, only the foreign substance When there is no light having a wavelength that excites the light, there is a problem that foreign matter cannot be specified.

  The present invention has been made to solve such a problem, and eliminates bright spots caused by foreign substances without going through complicated steps, and enables accurate fluorescent image detection from a fluorescent substance to be detected. It is an object of the present invention to provide an image reading method and apparatus that can perform the above-described process.

According to the present invention,
An image reading method for reading a fluorescent image from a capillary array sheet in which through holes containing different types of probes are arranged in a predetermined pattern, and a specimen to which a fluorescent material is applied is selectively bonded to the probe. ,
Irradiating the capillary array sheet with light to capture a transmission image of each through hole; and
Irradiating the capillary array sheet with excitation light having a wavelength that can excite the fluorescent material, and capturing a fluorescent image by fluorescence emitted from the fluorescent material;
Dividing the image data of the fluorescence image into fluorescence image data groups for each through hole based on the transmission image and the fluorescence image;
Calculating a threshold value for each through hole from the fluorescent image data group for each through hole;
For each of the through holes, based on the threshold value of the through hole, the step of eliminating the fluorescence image data by the bright spot from the fluorescence image data group of the through hole,
The threshold is
Median + (third quartile-first quartile) × a (where 1 <a ≦ 2)
An outlier represented by
Median value xb (1 <b ≦ 3)
Including the limit value represented by
In the exclusion step, when image data exceeding the limit value is included in the image data group, image data larger than the outlier is determined as image data by a bright spot and is excluded, and the image data group When image data exceeding the limit value is not included, it is determined that the image data group does not include image data based on bright spots.
An image reading method is provided.

According to such a configuration, it is possible to accurately detect a fluorescent image from a fluorescent material to be detected by eliminating a bright spot or the like due to a foreign substance without going through complicated steps.
Furthermore, according to such a configuration, even when the brightness difference in the image data group for each through hole is small (dispersion value is small), brighter image data is determined as a bright spot (noise). Exclusion is suppressed.

According to another aspect of the invention,
An image reading apparatus for reading a fluorescent image from a capillary array sheet in which through holes containing different types of probes are arranged in a predetermined pattern, and a specimen to which a fluorescent material is applied is selectively bonded to the probe. ,
A first light source for irradiating the capillary array sheet with light;
A second light source that irradiates the capillary array sheet with excitation light having a wavelength capable of exciting the fluorescent material;
First imaging means for capturing a transmission image of the capillary array sheet with light from the first light source;
Second imaging means for imaging a fluorescence image by fluorescence emitted from the fluorescent material by excitation light from the second light source;
Data dividing means for dividing the image data of the fluorescent image into fluorescent image data groups for each through hole based on the transmission image and the fluorescent image;
Threshold calculation means for calculating a threshold value for each through hole from the fluorescent image data group for each through hole;
Bright spot data excluding means for excluding fluorescent image data due to bright spots from the fluorescent image data group of the through hole based on the threshold value of the through hole for each through hole,
The threshold is
Median + (third quartile-first quartile) × a (where 1 <a ≦ 2)
An outlier represented by
Median value xb (1 <b ≦ 3)
Including the limit value represented by
In the bright spot data exclusion means, when the image data group includes image data exceeding the limit value, the image data larger than the outlier is determined to be bright spot image data and eliminated, and the image data When image data exceeding the limit value is not included in the data group, it is determined that the image data group does not include image data based on bright spots.
An image reading apparatus is provided.

According to such a configuration, it is possible to accurately detect a fluorescent image from a fluorescent material to be detected by eliminating a bright spot or the like due to a foreign substance without going through complicated steps.
Furthermore, according to such a configuration, even when the brightness difference in the image data group for each through hole is small (dispersion value is small), brighter image data is determined as a bright spot (noise). Exclusion is suppressed.

  According to the present invention, there is provided an image reading method and apparatus that eliminates a bright spot or the like caused by a foreign substance without going through complicated steps, and enables accurate detection of a fluorescent image from a fluorescent material to be detected. .

Hereinafter, a configuration of a reading apparatus according to a preferred embodiment of the present invention will be described with reference to the accompanying drawings.
FIG. 1 is a drawing schematically showing a configuration of an image reading apparatus according to a preferred embodiment of the present invention. The image reading apparatus 1 has a structure similar to that of a microscope, an objective lens 2, an XY stage 4 on which a capillary array sheet S to be read is placed, and a capillary array placed on the XY stage 4. An excitation light source 6 that irradiates excitation light on the front side surface of the sheet S and a transmission light source 8 that irradiates irradiation light from the back side of the capillary array sheet S placed on the XY stage 4 are provided.
The image reading device 1 further includes a fluorescence image by fluorescence emitted from the capillary array sheet S by light from the excitation light source 6 and a transmission image irradiated from the transmission light source 8 and transmitted through the capillary array sheet S. A CCD camera 10 is provided as an imaging means for imaging.

  The excitation light source 6 is configured to generate excitation light having a wavelength that excites a fluorescent substance attached to a sample that is hybridized with a probe accommodated in a through-hole of the capillary array sheet S. . The excitation light emitted from the excitation light source 6 passes through the excitation light filter 12, is deflected toward the capillary array sheet S by the dichroic mirror 14, and irradiates the front side surface of the capillary array sheet S. The fluorescent material applied to the sample hybridized with the probe accommodated in the through hole of the array sheet S is excited.

  Fluorescence emitted from the fluorescent material that labels the specimen bound to the probe in the through-hole of the capillary array sheet S passes through the dichroic mirror 14 and the absorption filter 16 and enters the CCD camera 10, where the CCD A fluorescent image of the capillary array sheet S is captured by the camera 10.

  The transmission light source 8 is disposed below the XY stage 4 so that the optical axis of the emitted light and the optical axis of the objective lens 2 coincide. As the transmissive light source 6, for example, a halogen lamp, an LED array light source, or the like can be used. From the viewpoint of stable light quantity and long life of the light source, it is preferable to use an LED array.

  The image reading device 1 further includes a data processing means 18 that processes and stores image data from the CCD camera 10 and a control device 20 that controls the operation of each component of the image reading device 1. The data processing means is constituted by a computer or the like in which a predetermined program is installed.

  The capillary array sheet S has a configuration in which a large number of capillaries having a through hole in the center are two-dimensionally arranged, and different types of biological substances (probes) are placed in the through holes of each capillary. The structure is fixed by a gel. In the capillary array sheet S, the through-hole filled with the gel transmits light, but the other portions do not substantially transmit light. In the image reading apparatus of this embodiment, image reading is performed from a capillary array sheet in which a specimen labeled with a fluorescent substance is selectively bound to a probe by hybridization or the like.

Next, an image reading method using the image reading apparatus 1 will be described.
First, the capillary array sheet S to be read is placed on the XY stage 4, irradiated with illumination light from the transmission light source 8, and an image (transmission image) of the transmission light transmitted through the capillary array sheet S is obtained. An image is taken by the CCD camera 10. Each image data of the transmission image is converted to a gradation value of 0 to 65535 according to the amount of light by A / D conversion, and sent to the data processing means 18.

  FIG. 2 shows a part of the obtained transmission image. As described above, since only the through holes transmit light in the capillary array sheet S, in the transmission image, substantially circular images 22, 24, 26, and 28 corresponding to the through holes are positions corresponding to the through holes. Appear in

  In the data processing means 18, the region where the image data of the through hole of the transmission image data is obtained is set as a detection region where the bright spot is eliminated in the fluorescent image.

  In the present embodiment, the image data of each through hole is separated from other image data based on a predetermined threshold value, and the region where the image data value of the separated through hole is obtained is specified. A circular area around the center of gravity of the area is set as a detection area for each through hole. The position data of each detection area set in this way is stored in the data processing means 18.

  Note that the region where the image data value of the through hole is obtained may be set as the detection region, or the detection region may be manually set by the operator.

  Next, the excitation light source 6 is actuated to irradiate the capillary array sheet S with excitation light to excite the fluorescent substance that labels the analyte selectively bonded to the probe of a specific through hole. A fluorescence image of fluorescence emitted from the fluorescent material is captured by the CCD camera 10.

  FIG. 3 is a fluorescence image corresponding to the transmission image of FIG. In the through-hole in which the specimen is bound to the probe, the fluorescent substance labeling the specimen is excited by the excitation light from the excitation light source 6, so that a bright image corresponding to the shape of the through-hole as shown in FIG. 24 '.

On the other hand, since there is no fluorescent substance in the portion corresponding to the through hole where the specimen is not bound to the probe, dark images 22 ′ and 26 ′ are obtained as shown in FIG.
Further, when a foreign substance excited by the excitation light from the excitation light source 6 exists in the through hole, as shown in FIG. 3, an image 28 ′ including fluorescence from the foreign substance as a bright spot 28 ″ is obtained.

  This fluorescent image data is also converted to a gradation value of 0 to 65535 according to the amount of light by A / D conversion, and is sent to the data processing means 18.

  The data processing means 18 performs a process for removing bright spots caused by foreign substances from the image data of the fluorescence image. In the present embodiment, since the removal of the bright spot due to the foreign matter is performed only in the detection region set based on the transmission image, based on the position data of the detection region stored in the data processing unit 18, Detection areas 30, 32, 34, and 36 are set in the fluorescence image data, and for each of the detection areas 30, 32, 34, and 36, processing for removing bright spots caused by foreign matters is performed as follows.

First, using Equation 1, threshold values (outliers) for the detection area used for the bright spot determination performed in each detection area are calculated from the values of the image data in the detection area arranged in ascending order. calculate.
Outlier = median + (third quartile−first quartile) × a Equation 1
Here, a is appropriately set within the range of (1 <a ≦ 2), and more preferably within the range of (1.2 <a ≦ 1.8).

  Here, the third quartile is, for example, the 75th data when 100 pieces of data are arranged in ascending order, and the first quartile is the 25th data.

Furthermore, the threshold value (limit value) for the detection region used for the bright spot determination performed in each detection region is calculated from the value of each image data in the detection region arranged in ascending order using Equation 2. calculate.
Limit value = median value × b (1 <b ≦ 3) Equation 2

  The limit value can be changed by changing the coefficient b. It is preferable to set b so that the bright spot noise can be appropriately excluded while referring to the obtained fluorescence image data, for example, in the range of (1.5 <b ≦ 2.5).

Next, for each detection area, the value (tone value) of each image data in the detection area is compared with the outlier value and the limit value, and whether the image data indicates a bright spot caused by a foreign object. Determine whether or not.
In the determination processing of this embodiment, when image data exceeding the limit value is included in the image data (image data group) in the detection area, image data larger than the outlier is determined as image data by a bright spot, while detection is performed. When image data exceeding the limit value is not included in the image data (image data group) in the area, it is determined that the image data in the detection area does not include image data based on bright spots. That is, it is determined whether or not image data based on a bright spot is included based on the limit value. If it is determined that image data based on a bright spot is included, which image data is determined based on the outlier. Is a bright spot.
Bright spot (noise) image data determined as image data indicating a bright spot is separated from other image data (image data group) in the detection area and excluded.

  When the outlier and the limit value exceed the saturation value of 65535, the bright spot determination is impossible, and hence the bright spot determination is not performed.

  FIG. 4 is an example of a fluorescence image in the vicinity of the detection region 40 including a bright spot caused by the foreign matter 38. FIG. 5 shows the image data of the fluorescence image in FIG. 4 arranged in ascending order according to the magnitude of the gradation value. It is a graph. In FIG. 5, image data in which the alternate long and short dash line indicates an outlier, the alternate long and two short dashes line indicates a saturation value, the dotted line indicates a limit value, and the hatched portion indicates image data.

  As shown in FIG. 5, in this example, the image data in the detection area includes image data having gradation values exceeding the limit value indicated by the dotted line, and thus is indicated by the alternate long and short dash line. Image data having a gradation value (fluorescence intensity) exceeding an outlier (the gradation value is greater than A) is determined as image data by a bright spot. At this time, as shown in FIG. 5, even saturated image data is correctly determined as image data based on bright spots.

  On the other hand, FIG. 6 is an example of a fluorescent image in the vicinity of the detection region 42 that does not include a bright spot caused by a foreign substance, and FIG. 7 is an arrangement of the fluorescent images in FIG. 6 in ascending order according to the magnitude of the gradation value. It is a graph. In FIG. 7, similarly to FIG. 5, the alternate long and short dash line indicates an outlier, and the dotted line indicates a limit value.

  In the example of FIGS. 6 and 7, the image data in the detection area does not include image data having a gradation value (fluorescence intensity) exceeding the limit value indicated by the dotted line. Image data based on bright spots is not included, and all image data is determined as normal image data.

  Thereafter, the image data determined to be image data based on the bright spot is processed to be excluded from other image data (image data group) of the detection area, and the image data group of the detection area after the exclusion process is completed. For example, a further process, for example, a process for calculating the average reading value by averaging the gradation values of the image data in each detection region and obtaining the concentration of the fluorescent substance is performed.

  The present invention is not limited to the above embodiments, and various modifications are possible within the scope of the invention described in the claims, and these are also included in the scope of the present invention.

Examples of the present invention will be described below.
As the capillary array sheet, Genopal (registered trademark) (228 spots) manufactured by Mitsubishi Rayon Co., Ltd. was used. In the capillary array sheet, 228 through holes (spot portions) are provided in a member that does not transmit light (matrix portion), and a probe is fixed in each through hole by a filled gel.

  After a sample labeled with a fluorescent substance was hybridized to the probe of the capillary array sheet, a transmission image and a fluorescence image of the spot portion were obtained using a DNA chip detector manufactured by Mitsubishi Rayon Co., Ltd. The illumination for taking a transmission image of the DNA chip detector was an LED, and was illuminated from below the chip. Moreover, the excitation light source for fluorescent image imaging was a mercury lamp, and epi-illumination excitation was performed from above the chip. Transmission images and fluorescence images were taken with a CCD camera above the chip.

FIG. 2 is a part of the captured transmission image and includes four spots. FIG. 3 shows a part of the captured fluorescent image, which is an image in the same range as FIG.
As is apparent from FIG. 3, a bright spot (noise) 28 ″ appears in the fluorescent image corresponding to the through hole in which the foreign matter exists.

  The transmission image of FIG. 2 was binarized, and a circular area centered on the center of gravity of the spot portion (white portion) of the binarized transmission image was determined as the detection area. In FIG. 3, detection areas corresponding to the images 22 ′, 24 ′, 26 ′, and 28 ′ of the respective through holes are indicated by 30, 32, 34, and 36, respectively.

In the bright spot determination, the image data in the detection regions 30, 32, 34, and 36 corresponding to the images 22 ′, 24 ′, 26 ′, and 28 ′ of the through holes are digitized.
The outlier value a is 1.5 and the limit value coefficient b is 2, and the outlier value and limit value for each detection area are calculated from the above formulas 1 and 2, respectively. Bright point determination using outliers and limit values as tone values) was performed, image data determined to be bright points was removed, and detection data was generated from the remaining image data.

  Each of the through-hole images 22 ′, 24 ′, and 26 ′ has the gradation values of all the image data smaller than the limit value, that is, the tone values of all the image data are equal to or less than the limit value. In the hole images 22 ′, 24 ′, and 26 ′, detection data is generated using all image data.

  FIG. 8 is an enlarged view of the through hole image 28 ′ in FIG. 3, and FIG. 9 shows the result of the bright spot determination for each image data of the through hole image 28 ′. Normal image data is indicated by #, and bright spot (noise) image data is indicated by ◯.

  The image 28 ′ of the through-hole includes image data whose gradation value exceeds the limit value. Therefore, the image data whose gradation value is larger than the outlier is determined as image data based on the bright spot, and is excluded. Detection data was generated using only the data. When the sample was analyzed using the obtained detection data, since there was no bright spot noise, a highly reliable and highly accurate analysis result could be obtained.

1 is a diagram schematically illustrating an image reading apparatus according to a preferred embodiment of the present invention. 2 is an example of a transmission image obtained by the image reading apparatus of FIG. 1. It is a fluorescence image corresponding to the transmission image of FIG. It is an example of the fluorescence image of the detection area | region containing the luminescent spot resulting from a foreign material. 5 is a graph in which image data of the fluorescent image in FIG. 4 are arranged in ascending order according to the magnitude of the gradation value. It is an example of the fluorescence image of the detection area | region which does not contain the bright spot resulting from a foreign material. It is the graph which arranged each image of the fluorescence image of FIG. 6 in ascending order according to the magnitude | size of the gradation value. FIG. 4 is an enlarged view of a through hole image 28 ′ in FIG. 3. The result of the bright spot determination for each image data of the image 28 'of the through hole is shown.

Explanation of symbols

S: Capillary array sheet 1: Image reading device 4: XY stage 6: Excitation light source 8: Transmission light source 10: CCD camera 18: Data processing means

Claims (2)

An image reading method for reading a fluorescent image from a capillary array sheet in which through holes containing different types of probes are arranged in a predetermined pattern, and a specimen to which a fluorescent material is applied is selectively bonded to the probe. ,
Irradiating the capillary array sheet with light to capture a transmission image of each through hole; and
Irradiating the capillary array sheet with excitation light having a wavelength that can excite the fluorescent material, and capturing a fluorescent image by fluorescence emitted from the fluorescent material;
Dividing the image data of the fluorescence image into fluorescence image data groups for each through hole based on the transmission image and the fluorescence image;
Calculating a threshold value for each through hole from the fluorescent image data group for each through hole;
For each of the through holes, based on the threshold value of the through hole, the step of eliminating the fluorescence image data by the bright spot from the fluorescence image data group of the through hole,
The threshold is
Median + (third quartile-first quartile) × a (where 1 <a ≦ 2)
An outlier represented by
Median value xb (1 <b ≦ 3)
Including the limit value represented by
In the exclusion step, when image data exceeding the limit value is included in the image data group, image data larger than the outlier is determined as image data by a bright spot and is excluded, and the image data group When image data exceeding the limit value is not included, it is determined that the image data group does not include image data based on bright spots.
An image reading method characterized by the above. An image reading apparatus for reading a fluorescent image from a capillary array sheet in which through holes containing different types of probes are arranged in a predetermined pattern, and a specimen to which a fluorescent material is applied is selectively bonded to the probe. ,
A first light source for irradiating the capillary array sheet with light;
A second light source that irradiates the capillary array sheet with excitation light having a wavelength capable of exciting the fluorescent material;
First imaging means for capturing a transmission image of the capillary array sheet with light from the first light source;
Second imaging means for imaging a fluorescence image by fluorescence emitted from the fluorescent material by excitation light from the second light source;
Data dividing means for dividing the image data of the fluorescent image into fluorescent image data groups for each through hole based on the transmission image and the fluorescent image;
Threshold calculation means for calculating a threshold value for each through hole from the fluorescent image data group for each through hole;
Bright spot data excluding means for excluding fluorescent image data due to bright spots from the fluorescent image data group of the through hole based on the threshold value of the through hole for each through hole,
The threshold is
Median + (third quartile-first quartile) × a (where 1 <a ≦ 2)
An outlier represented by
Median value xb (1 <b ≦ 3)
Including the limit value represented by
In the bright spot data exclusion means, when the image data group includes image data exceeding the limit value, the image data larger than the outlier is determined to be bright spot image data and eliminated, and the image data When image data exceeding the limit value is not included in the data group, it is determined that the image data group does not include image data based on bright spots.
An image reading apparatus.

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