CN117219235A - Processing method, system, equipment and medium for reading genetic FISH sample - Google Patents
Processing method, system, equipment and medium for reading genetic FISH sample Download PDFInfo
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Abstract
The invention provides a processing method, a system, equipment and a medium for reading a genetic FISH sample; according to the invention, a set of intelligent result input management system of the hereditary FISH subordinate project is developed and communicated with the KMCS laboratory subsystem, so that automatic film reading of the hereditary FISH in the laboratory and full-digital manufacturing management of the subordinate project result are realized, and the finished result pictures of the FISH subordinate project with a specified size are automatically generated and synchronized to the KMCS laboratory subsystem, and the automatic flow can greatly improve the film reading processing efficiency. The stereo detection and image processing algorithm can rapidly capture the image information of the sample, identify the probe signal and position the fluorescent marker probe, so that the data acquisition and analysis process is accelerated.
Description
Technical Field
The invention relates to the technical field of data processing, in particular to a method, a system, equipment and a medium for processing genetic FISH sample reading.
Background
The method comprises the steps that after a package item of a FISH post of a cytogenetic room is subjected to 70+ cases/month of the existing sample quantity, a subordinate item is subjected to 435 test/month, after a FISH comprehensive item is read manually, only pictures and comprehensive result suggestions can be uploaded in a comprehensive report KMCS system, when the result is required to be manually input, each item of probe information, a signal pattern diagram, an analysis result and a PPT which corresponds to the interpretation and input department and has a set size are input, each item of result is stored into a picture, and then the picture is uploaded to the KMCS system for previewing and issuing.
However, when the preview result finds that the error is completely returned, the result needs to be modified again, the picture needs to be saved, the picture needs to be uploaded, and the preview needs to be submitted, a series of operations need to be set up again through the system, and the input process is quite tedious and low in efficiency.
Disclosure of Invention
The invention aims to solve the problems that all the prior FISH chips are manually read, have strong subjectivity, are difficult to distinguish when encountering slides with poor signals, are recorded in a full-manual recording mode and proportion, and basically each package can be repeatedly returned and modified due to reasons such as punctuation errors, ratio summation being not equal to 100%, picture errors, mode writing errors and the like when auditing and issuing a bill, and provides a processing method, a system, equipment and a medium for reading genetic FISH samples.
The invention adopts the following technical means for solving the technical problems:
acquiring a pre-generated film reading sample, and identifying parameter content of the film reading sample based on a preset manual film reading mode, wherein the parameter content specifically comprises a fluorescent marker probe, a DNA sequence gene and the number of cell nucleuses;
judging whether the manual film reading mode needs to be expanded from Shan Zhangyue films to a plurality of films;
if yes, capturing an image of the film reading sample with high resolution by adopting preset three-dimensional detection, acquiring a probe signal of the film reading sample by adopting a preset image processing algorithm, detecting the probe signal of the fluorescent marked probe, performing signal positioning, identifying the signal of the DNA sequence gene according to the probe sequence of the fluorescent marked probe, calculating the number of cell nucleus signals of the film reading sample, identifying the cell density of the film reading sample according to the number of cell nucleus signals, and generating a three-dimensional FISH film reading corresponding to the three-dimensional detection;
Judging whether missing information exists in the three-dimensional FIS H film reading, wherein the missing information specifically comprises punctuation errors, pattern writing errors and proportion calculation errors;
if yes, the film reading sample is input into a preset text template, the detailed position of the missing information in the three-dimensional FIS H film reading is searched, the missing information is corrected based on the detailed position, and the corrected three-dimensional FISH film reading is regenerated.
Further, capturing the image of the film reading sample with high resolution by adopting a preset stereo detection, and before the step of acquiring the probe signal of the film reading sample by applying a preset image processing algorithm, further comprising:
performing image preprocessing on the image of the film reading sample to obtain a processed image, wherein the specific process of the image preprocessing comprises image denoising, image smoothing and color contrast balancing;
and adopting morphological operation to integrate the morphological structure of the processing image, removing the interference object in the processing image, and connecting the scattered signal areas in the processing image.
Further, the step of detecting the probe signal of the fluorescent-labeled probe and performing signal localization, and recognizing the signal of the DNA sequence gene according to the probe sequence of the fluorescent-labeled probe comprises:
Detecting the read sample by selecting a corresponding preset template based on a pre-selected subordinate item, wherein the subordinate item specifically comprises probe hybridization, signal detection and image acquisition, and the template specifically comprises a probe template and a signal mode template
Judging whether the template can finish the detection;
if not, increasing the fluorescent signal quantity of the fluorescent marked probe, correspondingly increasing the replication quantity of the probe marker, and simultaneously adjusting the experimental conditions of the read sample, wherein the experimental conditions specifically comprise hybridization temperature and hybridization time.
Further, before the step of determining whether the stereoscopic FISH reading piece has missing information, the method further includes:
calculating the yin-yang of the film reading sample based on the signal proportion of the film reading sample;
judging whether the yin and yang are leveled;
if yes, the detection intensity of the three-dimensional detection on the film reading sample is improved by applying preset signal amplification, wherein the signal amplification is specifically nanoparticle labeling or signal amplification.
Further, the step of inputting the film reading sample into a preset text template, searching the detailed position of the missing information in the stereoscopic FIS H film reading, correcting the missing information based on the detailed position, and regenerating the corrected stereoscopic FISH film reading includes:
Obtaining the sum of signal values of the three-dimensional FISH reading sheets;
judging whether the sum of the signal values matches a preset signal value or not;
if not, checking based on a detection stage corresponding to the signal value, and identifying the checked defect stage, wherein the detection stage specifically comprises signal detection, signal overlapping and signal miscalculation.
Further, the step of inputting the film reading sample into a preset text template, searching the detailed position of the missing information in the stereoscopic FIS H film reading, correcting the missing information based on the detailed position, and regenerating the corrected stereoscopic FISH film reading further comprises:
converting the corrected stereoscopic FISH reading into a visual picture form of cytogenetic FISH dependent project results;
judging whether the preset laboratory looks at the cytogenetic FISH subordinate project results;
if yes, synchronizing the cytogenetic FIS H subordinate project result to the preset laboratory, and finishing the input of the read sample.
The invention also provides a processing system for reading the genetic FISH sample, which comprises:
the acquisition module is used for acquiring a pre-generated film reading sample and identifying parameter content of the film reading sample based on a preset manual film reading mode, wherein the parameter content specifically comprises a fluorescence labeling probe, a DNA sequence gene and the number of cell nuclei;
The judging module is used for judging whether the manual film reading mode needs to be expanded into a plurality of film reading modes from Shan Zhangyue films or not;
the execution module is used for capturing the image of the film reading sample with high resolution by adopting preset three-dimensional detection if the image is detected, acquiring a probe signal of the film reading sample by adopting a preset image processing algorithm, detecting the probe signal of the fluorescent marker probe and carrying out signal positioning, identifying the signal of the DNA sequence gene according to the probe sequence of the fluorescent marker probe, calculating the number of cell nucleus signals of the film reading sample, identifying the cell density of the film reading sample according to the number of cell nucleus signals, and generating a three-dimensional FISH film reading corresponding to the three-dimensional detection;
the second judging module is used for judging whether missing information exists in the three-dimensional FISH reading sheet, wherein the missing information specifically comprises punctuation errors, pattern writing errors and proportion calculation errors;
and the second execution module is used for inputting the film reading sample into a preset text template if the film reading sample exists, searching the detailed position of the missing information in the three-dimensional FISH film reading, correcting the missing information based on the detailed position, and regenerating the corrected three-dimensional FISH film reading.
Further, the method further comprises the following steps:
the processing module is used for carrying out image preprocessing on the image of the film reading sample to obtain a processed image, wherein the specific process of the image preprocessing comprises image denoising, image smoothing and color contrast balancing;
and the integration module is used for integrating the morphological structure of the processing image by adopting morphological operation, removing interference objects in the processing image and connecting scattered signal areas in the processing image.
The invention also provides a computer device comprising a memory and a processor, the memory storing a computer program which, when executed by the processor, causes the processor to perform the steps of the method of processing a genetic FISH sample read as claimed in any one of claims 1 to 6.
The present invention also provides a computer-readable storage medium, characterized in that a computer program is stored, which, when being executed by a processor, causes the processor to perform the steps of the method for processing a genetic FISH sample reading as claimed in any one of claims 1 to 6.
The invention provides a processing method, a system, equipment and a medium for reading a genetic FISH sample, which have the following beneficial effects:
According to the invention, a set of intelligent result input management system of the hereditary FISH subordinate project is developed and communicated with the KMCS laboratory subsystem, so that automatic film reading of the hereditary FISH in the laboratory and full-digital manufacturing management of the subordinate project result are realized, and the finished result pictures of the FISH subordinate project with a specified size are automatically generated and synchronized to the KMCS laboratory subsystem.
Drawings
In order to more clearly illustrate the embodiments of the invention or the technical solutions in the prior art, the drawings that are required in the embodiments or the description of the prior art will be briefly described, it being obvious that the drawings in the following description are only some embodiments of the invention, and that other drawings may be obtained according to these drawings without inventive effort for a person skilled in the art.
Wherein:
FIG. 1 is a schematic flow chart of an embodiment of a method for processing a genetic FISH sample reading in accordance with the present invention;
FIG. 2 is a block diagram illustrating an exemplary embodiment of a genetic FISH sample reading processing system in accordance with the present invention;
FIG. 3 is a schematic diagram showing the internal structure of a computer device according to an embodiment of a method for processing a genetic FISH sample.
Detailed Description
The following description of the embodiments of the present invention will be made clearly and completely with reference to the accompanying drawings, in which it is apparent that the embodiments described are only some embodiments of the present invention, but not all embodiments. All other embodiments, which can be made by those skilled in the art based on the embodiments of the invention without making any inventive effort, are intended to be within the scope of the invention.
Referring to fig. 1, a method for processing a genetic FISH sample according to an embodiment of the present invention includes:
s1: acquiring a pre-generated film reading sample, and identifying parameter content of the film reading sample based on a preset manual film reading mode, wherein the parameter content specifically comprises a fluorescent marker probe, a DNA sequence gene and the number of cell nucleuses;
s2: judging whether the manual film reading mode needs to be expanded from Shan Zhangyue films to a plurality of films;
s3: if yes, capturing an image of the film reading sample with high resolution by adopting preset three-dimensional detection, acquiring a probe signal of the film reading sample by adopting a preset image processing algorithm, detecting the probe signal of the fluorescent marked probe, performing signal positioning, identifying the signal of the DNA sequence gene according to the probe sequence of the fluorescent marked probe, calculating the number of cell nucleus signals of the film reading sample, identifying the cell density of the film reading sample according to the number of cell nucleus signals, and generating a three-dimensional FISH film reading corresponding to the three-dimensional detection;
S4: judging whether missing information exists in the three-dimensional FIS H film reading, wherein the missing information specifically comprises punctuation errors, pattern writing errors and proportion calculation errors;
s5: if yes, the film reading sample is input into a preset text template, the detailed position of the missing information in the three-dimensional FIS H film reading is searched, the missing information is corrected based on the detailed position, and the corrected three-dimensional FISH film reading is regenerated.
In this embodiment, the system identifies the parameter content in the film reading sample by acquiring a pre-generated film reading sample and applying a pre-set manual film reading mode, including a fluorescent marker probe, a DNA sequence gene and the number of cell nuclei, and then the system judges whether the manual film reading mode needs to be expanded from a single film reading mode to a multiple film reading mode so as to execute the corresponding steps; for example, when the system determines that the manual film reading mode does not need to be expanded into a plurality of film reading modes by a single Zhang Yue film, the system can consider that the current film reading sample belongs to a clearer film reading sample, and can read the film reading sample in the manual film reading mode, so that an operator can clearly see the parameter content of the film reading sample to be recorded in the glass slide through naked eyes, and therefore, three-dimensional detection is not needed to detect the film reading sample; for example, when the system judges that the manual film reading mode needs to be expanded into a plurality of film reading modes by Shan Zhangyue films, the system indicates that an operator cannot see the contents of all film reading sample parameters to be recorded in a glass slide clearly through naked eyes, so that the system can capture images of the film reading samples with high resolution through a preset three-dimensional detection, acquire probe signals of fluorescent marked probes by using a preset image processing algorithm, acquire the probe signals of the fluorescent marked probes, then perform signal positioning on the probes, identify signals of DNA sequence genes according to the probe sequences of the fluorescent marked probes, calculate the number of cell nuclear signals in the film reading samples, and identify the cell density of the film reading samples according to the number of the cell nuclear signals, namely generate three-dimensional FISH film reading corresponding to three-dimensional detection; then the system judges whether missing information needing to be input in a supplementary mode exists in the three-dimensional FIS H film reading or not so as to execute corresponding steps; for example, when the system determines that the three-dimensional FIS H reading sheet does not have missing information which needs to be input in a supplementing mode, the system can consider that the three-dimensional FISH reading sheet can accurately capture and identify information such as signals, probe sequences, cell nucleus number and the like in a sample, so that missing information is avoided, and the missing information can be directly and synchronously uploaded to a laboratory for inputting data; for example, when the system determines that the three-dimensional FIS H reading has missing information which needs to be input in a supplementary mode, at the moment, the system inputs a reading sample into a preset text template, searches detailed positions of the missing information in the three-dimensional FIS H reading, and correspondingly corrects the missing information based on the detailed positions, so that the corrected three-dimensional FIS H reading can be regenerated.
It should be noted that, because the cells are three-dimensional, the information seen by the person reading is often only one side, and the sample of the person reading can be expanded into a plurality of pictures to determine the detection result together, for example, some of the sample of the person reading may be impurities, and if the sample of the person reading may not be well separated, the sample of the person reading can be detected and confirmed through the plurality of pictures, so that the accuracy of the detection is improved, but because the sample of the person reading needs to be expanded into the plurality of pictures, uncertainty still exists in the manner of the person reading, and the accuracy of 100% cannot be achieved.
The method comprises the steps of acquiring probe signals in a film reading sample by using a preset image processing algorithm, detecting the probe signals of a fluorescent marked probe, then carrying out signal positioning on the probe, and according to the signals of DNA sequence genes identified by the probe sequences of the fluorescent marked probe, calculating the number of cell nucleus signals in the film reading sample, wherein the specific process for identifying the cell density of the film reading sample according to the number of the cell nucleus signals is as follows:
firstly, an image is acquired from a film reading sample, the image can be obtained through a microscope and other equipment, then the image is preprocessed, operations such as denoising, contrast enhancement and the like can be possibly included, the image is prepared for subsequent processing, then a preset image processing algorithm is used for signal detection, the algorithm analyzes the image to detect signals of fluorescent marker probes, other methods such as threshold segmentation and edge detection are used for positioning the positions of the fluorescent signals, then the signals of DNA sequence genes are identified by using probe sequence information of the probes on the basis of the fluorescent marker probe signals, the probe sequences are matched with target gene sequences, the probe sequences are corresponding to the positions of the fluorescent signals, signals of the DNA sequence genes are identified, and the number of cell nucleus signals identified in the film reading sample is counted. Each cell nucleus signal corresponds to the existence of one cell nucleus, the cell density in the read sample is identified through a threshold-based binarization method according to the number of the cell nucleus signals, the cell density is generally estimated by the number of the cell nuclei, and finally, the result of the read sample is generated according to the number of the cell nuclei signals and the cell density, and the result comprises information such as the number of the cell nuclei, the cell density, the distribution of DNA sequence gene signals and the like, and is presented in a digital data or image form.
In this embodiment, capturing the image of the film reading sample with high resolution by using a preset stereo detection, and before the step S3 of collecting the probe signal of the film reading sample by using a preset image processing algorithm, further includes:
s30 1: performing image preprocessing on the image of the film reading sample to obtain a processed image, wherein the specific process of the image preprocessing comprises image denoising, image smoothing and color contrast balancing;
s30 2: and adopting morphological operation to integrate the morphological structure of the processing image, removing the interference object in the processing image, and connecting the scattered signal areas in the processing image.
In the embodiment, after the system performs image preprocessing on the image of the film reading sample, the image denoising, image content smoothing and image color saturation and contrast balancing are performed on the image, and the preprocessing process adopts pytho n to perform operation, so that a processed image is obtained after the operation is completed; and then the system integrates the morphological structure of the processed image by adopting morphological operation so as to remove the interference objects existing in the processed image and connect the scattered signal areas in the processed image.
It should be noted that the operation procedure using python is exemplified as follows:
Removing noise from an image, applying a Gaussian filter to reduce random interference
Example code (using Python):
import cv2
image＝cv2.imread("sample_image.jpg")
denoised_image＝cv2.GaussianBlur(image,(3,3),0)；
smoothing the image helps to remove fine texture and noise, making the signal more prominent by using an averaging filter, example codes are:
smoothed_image＝cv2.medianBlur(denoised_image,3)；
enhancing the color saturation and contrast of the image, making the signal more visible, by adjusting the pixel distribution of the image using a histogram equalization method, example codes are:
equalized_image＝cv2.equalizeHist(smoothed_image)；
finally, the preprocessed image is saved for subsequent analysis, with example code of:
cv2.imwrite("preprocessed_image.jpg",equalized_image)。
the specific procedure of integrating the processed images by morphological operations is exemplified as follows:
firstly, reading an image needing morphological operation, if the image is not a binary image (black-and-white image), binarizing the image, marking a region of interest as white (foreground), marking the rest as black (background), applying expansion operation to the binary image, sliding the white region on the image by using a structural element, expanding the white region, and being beneficial to filling a small cavity and connecting adjacent parts;
example code (using Python):
import cv2
import numpy as np
image＝cv2.imread("binary_image.jpg",cv2.IMREAD_GRAYSCALE)
kernel=np.ones ((5, 5), np.uint 8) # defines the structural element of the expansion operation
dilated_image＝cv2.dilate(image,kernel,iterations＝1)；
Applying a corrosion operation to the inflated image to reduce the white area and smooth the edge of the image
Example code (using Python):
kernel=np.ones ((3, 3), np.uint 8) # defines the structural element of the etching operation
closed_image＝cv2.erode(dilated_image,kernel,iterations＝1)
Finally, the image after morphological operation processing is saved
Example code (using Python):
cv2.imwrite("closed_image.jpg",closed_image)。
in this embodiment, the step S3 of detecting the probe signal of the fluorescent-labeled probe and performing signal localization to identify the signal of the DNA sequence gene from the probe sequence of the fluorescent-labeled probe includes:
s3 1: detecting the film reading sample by selecting a corresponding preset template based on a pre-selected subordinate item, wherein the subordinate item specifically comprises probe hybridization, signal detection and image acquisition, and the template specifically comprises a probe template and a signal mode template;
s32: judging whether the template can finish the detection;
s3 3: if not, increasing the fluorescent signal quantity of the fluorescent marked probe, correspondingly increasing the replication quantity of the probe marker, and simultaneously adjusting the experimental conditions of the read sample, wherein the experimental conditions specifically comprise hybridization temperature and hybridization time
In this embodiment, the system selects corresponding preset templates based on the content of the pre-selected subordinate item to detect the film reading sample, and then determines whether the templates can successfully complete detection so as to execute corresponding steps; for example, when the system determines that the template can complete detection, the system calculates relevant information of the film reading sample according to the yin-yang judgment threshold value set in the template, and the yin-yang judgment threshold value is a limit, so that the system can be used for judging negative and positive conditions of signals in the film reading sample, and accordingly result classification is performed; for example, when the system determines that the detection cannot be completed by the template, the system increases the number of fluorescent signals of the fluorescent labeled probe and correspondingly increases the replication number of the probe markers, so as to improve the detection sensitivity of the signals and the detection probability of the target sequence, and simultaneously adjusts the hybridization temperature and hybridization time of the read sample, thereby improving the hybridization efficiency and stability of the probe and the target sequence.
In this embodiment, before step S4 of determining whether missing information exists in the stereoscopic FISH reading sheet, the method further includes:
s401: calculating the yin-yang of the film reading sample based on the signal proportion of the film reading sample;
s402: judging whether the yin and yang are leveled;
s40, 3: if yes, the detection intensity of the three-dimensional detection on the film reading sample is improved by applying preset signal amplification, wherein the signal amplification is specifically nanoparticle labeling or signal amplification.
In this embodiment, the system calculates the yin-yang property of the film-reading sample based on the signal value ratio of the film-reading sample, and then the system judges whether the yin-yang property has a leveling condition or not to execute the corresponding steps; for example, when the system determines that the yin and yang are not sustained, the system considers that the read sample has obvious negative or positive, reflecting the relative proportion of negative and positive cells in the sample, so the read sample belongs to a normal cytogenetic FISH sample; for example, when the system determines that a positive-negative is on average, the system will then apply a pre-configured nanoparticle label to increase the detection intensity of the stereoscopic image on the read sample, as the nanoparticle label generally has good stability, controllability and adjustable surface chemistry, so that the labeled nanoparticle can be bound directionally to the target sequence, some nanoparticle labeling techniques allow for labeling multiple nanoparticles on a single target, thereby increasing the number and intensity of signals.
It should be noted that, specific examples of calculating the yin and yang of the film reading sample are as follows:
firstly, counting signals of each cell in an image, assuming that fluorescent signals are concerned, each signal represents the existence of a gene, setting a negative and positive judgment threshold value for defining the proportion of negative and positive signals, setting the threshold value according to the characteristics of experiments and expected results, calculating the proportion of the number of the signals to the number of cell nuclei in a read sample for each cell to obtain a signal proportion value, classifying the cells into negative and positive according to the signal proportion value, classifying the cells with the proportion lower than the threshold value as negative, classifying the cells with the proportion higher than the threshold value as positive, counting the number of the cells classified by yin and yang, and comprehensively judging the yin and yang of the whole sample according to other information such as the cell number and cell morphology.
Example description:
assuming that a set of cytogenetic FIS H images were analyzed, wherein each cell contained a fluorescent signal for a specific gene, the system set a yin-yang judgment threshold of 0.5, i.e., positive when the signal ratio was above 0.5, negative when it was below 0.5;
there were 10 signals in cell a and the number of nuclei was 2 0. The signal ratio was 10/20=0.5, equal to the threshold, and was judged to be positive.
There were 5 signals in cell B and the number of nuclei was 1 5. The signal ratio was 5/15.apprxeq.0.3, below the threshold, and was judged negative.
According to the judgment of the signal proportion, the cell A is judged to be positive, the cell B is judged to be negative, and according to the classification results of all cells, the negative and positive of the whole film reading sample can be calculated.
In this embodiment, the step S5 of inputting the film reading sample into a preset text template, searching the detailed position of the missing information in the stereoscopic FIS H film reading, correcting the missing information based on the detailed position, and regenerating the corrected stereoscopic FISH film reading includes:
s51: obtaining the sum of signal values of the three-dimensional FISH reading sheets;
s52: judging whether the sum of the signal values matches a preset signal value or not;
s5 3: if not, checking based on a detection stage corresponding to the signal value, and identifying the checked defect stage, wherein the detection stage specifically comprises signal detection, signal overlapping and signal miscalculation.
In this embodiment, the system acquires the sum of the signal values in the stereoscopic FISH reading sheet, and then determines whether the sum of the signal values matches a preset signal value, so as to execute a corresponding step; for example, when the system determines that the sum of the signal values can match the preset signal value, it means that the number of signals detected by the system matches the expected number of signals in the analysis process of cytogenetic FIS H, when the sum of the signal values matches the preset signal value, it indicates that the gene of interest is actually present in the sample, and when the sum of the signal values matches the preset value, it can confirm that some chromosome structures exist, which indicates that the experimental technical operation and the signal analysis process are accurate; for example, when the system determines that the sum of the signal values cannot match the preset signal value, the system performs verification based on the detection stage corresponding to the signal value at this time, and identifies the defect stage obtained by the verification.
It should be noted that, specific examples of verifying and identifying the defect phase are as follows:
assuming that the system is analyzing for the presence of a particular gene and that there is a set of cytogenetic FIS H images, first a signal value threshold is set based on experimental and expected results, which can be used to determine if a signal is present, and the intensity of the signal; and then, carrying out signal value analysis on each cell image, judging whether each cell has a signal or not according to a set threshold value, wherein the detection stage is used for preliminarily determining whether the signal exists or not, then comparing the signal value obtained by analysis with an actual expected result, if the signal value is not consistent with the expected result, further checking and investigation are needed, if the difference between the signal value and the expected result is found in the comparison analysis, the defect stages can be considered and identified, such as whether the signal is correctly detected and positioned, the problems of signal omission detection, false detection and positioning error can occur, such as whether the cell nucleus segmentation is accurate, the problems of cell nucleus failure in correct segmentation and segmentation offset can occur, such as the accuracy of signal intensity measurement is checked, and the problems of inaccurate signal intensity measurement and fluorescence intensity saturation can occur.
In this embodiment, the step S5 of inputting the film reading sample into a preset text template, searching the detailed position of the missing information in the stereoscopic FIS H film reading, correcting the missing information based on the detailed position, and regenerating the corrected stereoscopic FISH film reading further includes:
s50 1: converting the corrected stereoscopic FISH reading into a visual picture form of a cytogenetic FIS H dependent project result;
s502: judging whether the preset laboratory looks at the cytogenetic FISH subordinate project results;
s50, 3: if yes, synchronizing the cytogenetic FIS H subordinate project result to the preset laboratory, and finishing the input of the read sample.
In this embodiment, the system converts the corrected stereoscopic FIS H reading into a visible picture form of the cytogenetic FIS H dependent item result required to be entered in the laboratory, and then determines whether the laboratory can view the cytogenetic FISH dependent item result to execute the corresponding steps; for example, when the system judges that the laboratory cannot view the result of the cytogenetic FIS H dependent project, the system considers that the problems of inaccurate device calibration and incorrect positioning exist when the automatic equipment is used for film reading, and after the equipment is required to be calibrated and tested, synchronous uploading is carried out again, so that the accuracy of an automatic process is ensured; for example, when the system determines that the laboratory can view the cytogenetic FISH subordinate project results, the system can successfully synchronize the cytogenetic FISH subordinate project results into the laboratory, and thus the entry of the read sample can be completed.
In summary, all the FIS H slides are currently manually read, so that subjectivity is strong, and the slides with poor signals are difficult to distinguish by naked eyes. The result is input into a full-manual input mode and proportion, basically every package can be repeatedly returned to the experiment due to the reasons of punctuation errors, summation of the ratios not equal to 100%, picture errors, mode writing errors and the like when the package is audited and sent out, and the system is saved again after the content in the PP T is modified again. After the system is used, the automatic verification function of the system and the function of the fully-automatic generated text template can eliminate the existing punctuation errors, pattern writing errors, proportion calculation errors and the like by 100%, reduce return operation and improve the result input accuracy to 100%.
Referring to FIG. 2, a system for processing a genetic FISH sample read in accordance with an embodiment of the present invention includes:
the acquisition module 10 is used for acquiring a pre-generated film reading sample and identifying parameter content of the film reading sample based on a preset manual film reading mode, wherein the parameter content specifically comprises a fluorescence labeling probe, a DNA sequence gene and the number of cell nuclei;
the judging module 20 is used for judging whether the manual film reading mode needs to be expanded into a plurality of film reading modes from Shan Zhangyue films;
The execution module 3 0 is configured to capture an image of the film reading sample with high resolution by adopting a preset stereo detection if the image is detected, acquire a probe signal of the film reading sample by adopting a preset image processing algorithm, detect the probe signal of the fluorescent marker probe, perform signal positioning, calculate the number of nuclear signals of the film reading sample according to the signal of the DNA sequence gene identified by the probe sequence of the fluorescent marker probe, identify the cell density of the film reading sample according to the number of the nuclear signals, and generate a stereo FISH film reading corresponding to the stereo detection;
the second judging module 4 0 is configured to judge whether missing information exists in the stereoscopic FISH reading sheet, where the missing information specifically includes punctuation errors, pattern writing errors and proportion calculation errors;
and the second execution module 5 0 is used for inputting the film reading sample into a preset text template if the film reading sample exists, searching the detailed position of the missing information in the three-dimensional FISH film reading, correcting the missing information based on the detailed position, and regenerating the corrected three-dimensional FISH film reading.
In this embodiment, the system identifies the parameter content in the film reading sample by acquiring a pre-generated film reading sample and applying a pre-set manual film reading mode, including a fluorescent marker probe, a DNA sequence gene and the number of cell nuclei, and then the system judges whether the manual film reading mode needs to be expanded from a single film reading mode to a multiple film reading mode so as to execute the corresponding steps; for example, when the system determines that the manual film reading mode does not need to be expanded into a plurality of film reading modes by a single Zhang Yue film, the system can consider that the current film reading sample belongs to a clearer film reading sample, and can read the film reading sample in the manual film reading mode, so that an operator can clearly see the parameter content of the film reading sample to be recorded in the glass slide through naked eyes, and therefore, three-dimensional detection is not needed to detect the film reading sample; for example, when the system judges that the manual film reading mode needs to be expanded into a plurality of film reading modes by Shan Zhangyue films, the system indicates that an operator cannot see the contents of all film reading sample parameters to be recorded in a glass slide clearly through naked eyes, so that the system can capture images of the film reading samples with high resolution through a preset three-dimensional detection, acquire probe signals of fluorescent marked probes by using a preset image processing algorithm, acquire the probe signals of the fluorescent marked probes, then perform signal positioning on the probes, identify signals of DNA sequence genes according to the probe sequences of the fluorescent marked probes, calculate the number of cell nuclear signals in the film reading samples, and identify the cell density of the film reading samples according to the number of the cell nuclear signals, namely generate three-dimensional FISH film reading corresponding to three-dimensional detection; then the system judges whether missing information needing to be input in a supplementary mode exists in the three-dimensional FIS H film reading or not so as to execute corresponding steps; for example, when the system determines that the three-dimensional FIS H reading sheet does not have missing information which needs to be input in a supplementing mode, the system can consider that the three-dimensional FISH reading sheet can accurately capture and identify information such as signals, probe sequences, cell nucleus number and the like in a sample, so that missing information is avoided, and the missing information can be directly and synchronously uploaded to a laboratory for inputting data; for example, when the system determines that the three-dimensional FIS H reading has missing information which needs to be input in a supplementary mode, at the moment, the system inputs a reading sample into a preset text template, searches detailed positions of the missing information in the three-dimensional FIS H reading, and correspondingly corrects the missing information based on the detailed positions, so that the corrected three-dimensional FIS H reading can be regenerated.
In this embodiment, further comprising:
the processing module is used for carrying out image preprocessing on the image of the film reading sample to obtain a processed image, wherein the specific process of the image preprocessing comprises image denoising, image smoothing and color contrast balancing;
and the integration module is used for integrating the morphological structure of the processing image by adopting morphological operation, removing interference objects in the processing image and connecting scattered signal areas in the processing image.
In the embodiment, after the system performs image preprocessing on the image of the film reading sample, the image denoising, image content smoothing and image color saturation and contrast balancing are performed on the image, and the preprocessing process adopts pytho n to perform operation, so that a processed image is obtained after the operation is completed; and then the system integrates the morphological structure of the processed image by adopting morphological operation so as to remove the interference objects existing in the processed image and connect the scattered signal areas in the processed image.
It should be noted that the operation procedure using python is exemplified as follows:
removing noise from an image, applying a Gaussian filter to reduce random interference
Example code (using Python):
import cv2
image＝cv2.imread("sample_image.jpg")
denoised_image＝cv2.GaussianBlur(image,(3,3),0)；
smoothing the image helps to remove fine texture and noise, making the signal more prominent by using an averaging filter, example codes are:
smoothed_image＝cv2.medianBlur(denoised_image,3)；
Enhancing the color saturation and contrast of the image, making the signal more visible, by adjusting the pixel distribution of the image using a histogram equalization method, example codes are:
equalized_image＝cv2.equalizeHist(smoothed_image)；
finally, the preprocessed image is saved for subsequent analysis, with example code of:
cv2.imwrite("preprocessed_image.jpg",equalized_image)。
the specific procedure of integrating the processed images by morphological operations is exemplified as follows:
firstly, reading an image needing morphological operation, if the image is not a binary image (black-and-white image), binarizing the image, marking a region of interest as white (foreground), marking the rest as black (background), applying expansion operation to the binary image, sliding the white region on the image by using a structural element, expanding the white region, and being beneficial to filling a small cavity and connecting adjacent parts;
example code (using Python):
import cv2
import numpy as np
image＝cv2.imread("binary_image.jpg",cv2.IMREAD_GRAYSCALE)
kernel=np.ones ((5, 5), np.uint 8) # defines the structural element of the expansion operation
dilated_image＝cv2.dilate(image,kernel,iterations＝1)；
Applying a corrosion operation to the inflated image to reduce the white area and smooth the edge of the image
Example code (using Python):
kernel=np.ones ((3, 3), np.uint 8) # defines the structural element of the etching operation
closed_image＝cv2.erode(dilated_image,kernel,iterations＝1)
Finally, the image after morphological operation processing is saved
Example code (using Python):
cv2.imwrite("closed_image.jpg",closed_image)。
In this embodiment, the execution module further includes:
the detection unit is used for detecting the film reading sample by selecting a corresponding preset template based on a pre-selected subordinate item, wherein the subordinate item specifically comprises probe hybridization, signal detection and image acquisition, and the template specifically comprises a probe template and a signal mode template;
the judging unit is used for judging whether the template can finish the detection;
and the execution unit is used for increasing the fluorescent signal quantity of the fluorescent marked probe if not, correspondingly increasing the replication quantity of the probe marker and simultaneously adjusting the experimental conditions of the read sample, wherein the experimental conditions specifically comprise hybridization temperature and hybridization time.
In this embodiment, the system selects corresponding preset templates based on the content of the pre-selected subordinate item to detect the film reading sample, and then determines whether the templates can successfully complete detection so as to execute corresponding steps; for example, when the system determines that the template can complete detection, the system calculates relevant information of the film reading sample according to the yin-yang judgment threshold value set in the template, and the yin-yang judgment threshold value is a limit, so that the system can be used for judging negative and positive conditions of signals in the film reading sample, and accordingly result classification is performed; for example, when the system determines that the detection cannot be completed by the template, the system increases the number of fluorescent signals of the fluorescent labeled probe and correspondingly increases the replication number of the probe markers, so as to improve the detection sensitivity of the signals and the detection probability of the target sequence, and simultaneously adjusts the hybridization temperature and hybridization time of the read sample, thereby improving the hybridization efficiency and stability of the probe and the target sequence.
In this embodiment, further comprising:
the calculating module is used for calculating the yin and yang of the film reading sample based on the signal proportion of the film reading sample;
the third judging module is used for judging whether the yin and yang are leveled or not;
and the third execution module is used for improving the detection intensity of the three-dimensional detection on the film reading sample by applying preset signal amplification if the film reading sample is detected, wherein the signal amplification is specifically nanoparticle marking or signal amplification.
In this embodiment, the system calculates the yin-yang property of the film-reading sample based on the signal value ratio of the film-reading sample, and then the system judges whether the yin-yang property has a leveling condition or not to execute the corresponding steps; for example, when the system determines that the yin and yang are not sustained, the system considers that the read sample has obvious negative or positive, reflecting the relative proportion of negative and positive cells in the sample, so the read sample belongs to a normal cytogenetic FISH sample; for example, when the system determines that a positive-negative is on average, the system will then apply a pre-configured nanoparticle label to increase the detection intensity of the stereoscopic image on the read sample, as the nanoparticle label generally has good stability, controllability and adjustable surface chemistry, so that the labeled nanoparticle can be bound directionally to the target sequence, some nanoparticle labeling techniques allow for labeling multiple nanoparticles on a single target, thereby increasing the number and intensity of signals.
In this embodiment, the second execution module further includes:
an acquisition unit for acquiring the sum of the signal values of the three-dimensional FISH reading sheets;
the second judging unit is used for judging whether the sum of the signal values is matched with a preset signal value or not;
and the second execution unit is used for checking based on the detection stage corresponding to the signal value if not, and identifying the checked defect stage, wherein the detection stage specifically comprises signal detection, signal overlapping and signal miscalculation.
In this embodiment, the system acquires the sum of the signal values in the stereoscopic FISH reading sheet, and then determines whether the sum of the signal values matches a preset signal value, so as to execute a corresponding step; for example, when the system determines that the sum of the signal values can match the preset signal value, it means that the number of signals detected by the system matches the expected number of signals in the analysis process of cytogenetic FIS H, when the sum of the signal values matches the preset signal value, it indicates that the gene of interest is actually present in the sample, and when the sum of the signal values matches the preset value, it can confirm that some chromosome structures exist, which indicates that the experimental technical operation and the signal analysis process are accurate; for example, when the system determines that the sum of the signal values cannot match the preset signal value, the system performs verification based on the detection stage corresponding to the signal value at this time, and identifies the defect stage obtained by the verification.
In this embodiment, further comprising:
the conversion module is used for converting the corrected stereoscopic FISH reading sheet into a visible picture form of a cytogenetic FIS H dependent project result;
a fourth judging module, configured to judge whether the preset laboratory views the cytogenetic FISH subordinate project result;
and the fourth execution module is used for synchronizing the cytogenetic FISH subordinate project result to the preset laboratory if yes, and finishing the recording of the film reading sample.
In this embodiment, the system converts the corrected stereoscopic FIS H reading into a visible picture form of the cytogenetic FIS H dependent item result required to be entered in the laboratory, and then determines whether the laboratory can view the cytogenetic FISH dependent item result to execute the corresponding steps; for example, when the system judges that the laboratory cannot view the result of the cytogenetic FIS H dependent project, the system considers that the problems of inaccurate device calibration and incorrect positioning exist when the automatic equipment is used for film reading, and after the equipment is required to be calibrated and tested, synchronous uploading is carried out again, so that the accuracy of an automatic process is ensured; for example, when the system determines that the laboratory can view the cytogenetic FISH subordinate project results, the system can successfully synchronize the cytogenetic FISH subordinate project results into the laboratory, and thus the entry of the read sample can be completed.
FIG. 3 illustrates an internal block diagram of a computer device in one embodiment. The computer device may specifically be a terminal or a server. As shown in fig. 3, the computer device includes a processor, a memory, and a network interface connected by a system bus. The memory includes a nonvolatile storage medium and an internal memory. The non-volatile storage medium of the computer device has a storage operating system and may also have a computer program, which when executed by the processor, causes the processor to implement a method for processing a genetic FIS H sample read as described above. The internal memory may also store a computer program which, when executed by the processor, causes the processor to perform a method of processing a genetic FISH sample read as described above. It will be appreciated by persons skilled in the art that the structure shown in fig. 3 is merely a block diagram of a portion of the structure associated with the present application and is not limiting of the apparatus to which the present application is applied, and that a particular apparatus may include more or fewer components than shown, or may combine certain components, or have a different arrangement of components.
In one embodiment, a computer device is provided that includes a memory and a processor, the memory having stored thereon a computer program that, when executed by the processor, causes the processor to perform the steps of the above-described method of processing a genetic FISH sample.
In one embodiment, a computer readable storage medium is provided, having a computer program stored therein, which when executed by a processor causes the processor to perform the steps of a method for processing a genetic FISH sample read as described above.
It will be appreciated that the above-described processing method, system, apparatus and medium for reading a genetic FIS H sample, system, computer apparatus and computer readable storage medium are all of a general inventive concept, and the embodiments are mutually applicable.
Those skilled in the art will appreciate that all or part of the processes in the methods of the above embodiments may be implemented by a computer program for instructing relevant hardware, where the program may be stored in a non-volatile computer readable storage medium, and where the program, when executed, may include processes in the embodiments of the methods described above. Any reference to memory, storage, database, or other medium used in embodiments provided herein may include non-volatile and/or volatile memory. The nonvolatile memory can include Read Only Memory (ROM), programmable ROM (PROM), electrically Programmable ROM (EPROM), electrically Erasable Programmable ROM (EEPROM), or flash memory. Volatile memory can include Random Access Memory (RAM) or external cache memory. By way of illustration and not limitation, RAM is available in a variety of forms such as Static RAM (SRAM), dynamic RAM (DRAM), synchronous DRAM (SDRAM), double Data Rate SDRAM (DDRSDRAM), enhanced SDRAM (ESDRAM), synchronous Link DRAM (SLDRAM), memory bus direct RAM (RDRAM), direct memory bus dynamic RAM (DRDRAM), and memory bus dynamic RAM (RDRAM), among others.
The technical features of the above embodiments may be arbitrarily combined, and all possible combinations of the technical features in the above embodiments are not described for brevity of description, however, as long as there is no contradiction between the combinations of the technical features, they should be considered as the scope of the description.
The foregoing examples illustrate only a few embodiments of the application and are described in detail herein without thereby limiting the scope of the application. It should be noted that it will be apparent to those skilled in the art that several variations and modifications can be made without departing from the spirit of the application, which are all within the scope of the application. Accordingly, the scope of protection of the present application is to be determined by the appended claims.
Claims (10)
1. The processing method of the genetic FISH sample reading is characterized by comprising the following steps:
acquiring a pre-generated film reading sample, and identifying parameter content of the film reading sample based on a preset manual film reading mode, wherein the parameter content specifically comprises a fluorescent marker probe, a DNA sequence gene and the number of cell nucleuses;
judging whether the manual film reading mode needs to be expanded from Shan Zhangyue films to a plurality of films;
If yes, capturing an image of the film reading sample with high resolution by adopting preset three-dimensional detection, acquiring a probe signal of the film reading sample by adopting a preset image processing algorithm, detecting the probe signal of the fluorescent marked probe, performing signal positioning, identifying the signal of the DNA sequence gene according to the probe sequence of the fluorescent marked probe, calculating the number of cell nucleus signals of the film reading sample, identifying the cell density of the film reading sample according to the number of cell nucleus signals, and generating a three-dimensional FISH film reading corresponding to the three-dimensional detection;
judging whether missing information exists in the three-dimensional FIS H film reading, wherein the missing information specifically comprises punctuation errors, pattern writing errors and proportion calculation errors;
if yes, the film reading sample is input into a preset text template, the detailed position of the missing information in the three-dimensional FIS H film reading is searched, the missing information is corrected based on the detailed position, and the corrected three-dimensional FISH film reading is regenerated.
2. The method for processing a read-out image of a genetic FISH sample according to claim 1, wherein the step of capturing the image of the read-out image with high resolution using a preset stereo detection and acquiring a probe signal of the read-out image using a preset image processing algorithm further comprises:
Performing image preprocessing on the image of the film reading sample to obtain a processed image, wherein the specific process of the image preprocessing comprises image denoising, image smoothing and color contrast balancing;
and adopting morphological operation to integrate the morphological structure of the processing image, removing the interference object in the processing image, and connecting the scattered signal areas in the processing image.
3. The method according to claim 1, wherein the step of detecting the probe signal of the fluorescent-labeled probe and performing signal localization to identify the signal of the DNA sequence gene based on the probe sequence of the fluorescent-labeled probe comprises:
detecting the film reading sample by selecting a corresponding preset template based on a pre-selected subordinate item, wherein the subordinate item specifically comprises probe hybridization, signal detection and image acquisition, and the template specifically comprises a probe template and a signal mode template;
judging whether the template can finish the detection;
if not, increasing the fluorescent signal quantity of the fluorescent marked probe, correspondingly increasing the replication quantity of the probe marker, and simultaneously adjusting the experimental conditions of the read sample, wherein the experimental conditions specifically comprise hybridization temperature and hybridization time.
4. The method for processing a genetic FISH sample page according to claim 1, wherein before the step of determining whether missing information exists in the stereoscopic FISH page, further comprising:
calculating the yin-yang of the film reading sample based on the signal proportion of the film reading sample;
judging whether the yin and yang are leveled;
if yes, the detection intensity of the three-dimensional detection on the film reading sample is improved by applying preset signal amplification, wherein the signal amplification is specifically nanoparticle labeling or signal amplification.
5. The method for processing a genetic FISH sample according to claim 1, wherein the step of inputting the sample into a preset text template, searching for a detailed position of the missing information in the stereoscopic FISH sample, correcting the missing information based on the detailed position, and regenerating a corrected stereoscopic FISH sample comprises:
obtaining the sum of signal values of the three-dimensional FISH reading sheets;
judging whether the sum of the signal values matches a preset signal value or not;
if not, checking based on a detection stage corresponding to the signal value, and identifying the checked defect stage, wherein the detection stage specifically comprises signal detection, signal overlapping and signal miscalculation.
6. The method for processing a genetic FISH sample according to claim 1, wherein the step of inputting the sample into a preset text template, searching for a detailed position of the missing information in the stereoscopic FISH sample, correcting the missing information based on the detailed position, and regenerating a corrected stereoscopic FISH sample further comprises:
converting the corrected stereoscopic FISH reading into a visual picture form of cytogenetic FISH dependent project results;
judging whether the preset laboratory looks at the cytogenetic FISH subordinate project results;
if yes, synchronizing the cytogenetic FIS H subordinate project result to the preset laboratory, and finishing the input of the read sample.
7. A genetic FISH sample read processing system, comprising:
the acquisition module is used for acquiring a pre-generated film reading sample and identifying parameter content of the film reading sample based on a preset manual film reading mode, wherein the parameter content specifically comprises a fluorescence labeling probe, a DNA sequence gene and the number of cell nuclei;
the judging module is used for judging whether the manual film reading mode needs to be expanded into a plurality of film reading modes from Shan Zhangyue films or not;
The execution module is used for capturing the image of the film reading sample with high resolution by adopting preset three-dimensional detection if the image is detected, acquiring a probe signal of the film reading sample by adopting a preset image processing algorithm, detecting the probe signal of the fluorescent marker probe and carrying out signal positioning, identifying the signal of the DNA sequence gene according to the probe sequence of the fluorescent marker probe, calculating the number of cell nucleus signals of the film reading sample, identifying the cell density of the film reading sample according to the number of cell nucleus signals, and generating a three-dimensional FISH film reading corresponding to the three-dimensional detection;
the second judging module is used for judging whether missing information exists in the three-dimensional FISH reading sheet, wherein the missing information specifically comprises punctuation errors, pattern writing errors and proportion calculation errors;
and the second execution module is used for inputting the film reading sample into a preset text template if the film reading sample exists, searching the detailed position of the missing information in the three-dimensional FISH film reading, correcting the missing information based on the detailed position, and regenerating the corrected three-dimensional FISH film reading.
8. The genetic FISH sample read processing system of claim 7, further comprising:
The processing module is used for carrying out image preprocessing on the image of the film reading sample to obtain a processed image, wherein the specific process of the image preprocessing comprises image denoising, image smoothing and color contrast balancing;
and the integration module is used for integrating the morphological structure of the processing image by adopting morphological operation, removing interference objects in the processing image and connecting scattered signal areas in the processing image.
9. A computer device comprising a memory and a processor, the memory storing a computer program which, when executed by the processor, causes the processor to perform the steps of the method of processing a genetic FISH sample read as claimed in any one of claims 1 to 6.
10. A computer-readable storage medium, in which a computer program is stored which, when executed by a processor, causes the processor to perform the steps of the method for processing a genetic FIS H sample read as claimed in any one of claims 1 to 6.
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