CN103914841A - Bacterium division and classification method based on superpixels and in-depth learning and application thereof - Google Patents

Bacterium division and classification method based on superpixels and in-depth learning and application thereof Download PDF

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CN103914841A
CN103914841A CN201410133805.3A CN201410133805A CN103914841A CN 103914841 A CN103914841 A CN 103914841A CN 201410133805 A CN201410133805 A CN 201410133805A CN 103914841 A CN103914841 A CN 103914841A
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bacterium
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super pixel
cut apart
classification
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CN103914841B (en
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汪天富
雷柏英
宋有义
曾忠铭
倪东
陈思平
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Shenzhen University
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Abstract

The invention provides a bacterium division and classification method based on superpixels and in-depth learning. The method comprises the steps that an in-depth learning classifier is established through a training image set, a tested image is compared with the in-depth learning classifier, and a classification result is output; the comparison comprises the steps that the tested image passes through all GRB channels to be subjected to median filtering, and noise is removed; the superpixels are calculated; the color, shape and dimension characteristics of each superpixel region are calculated; primary filtering is conducted on each superpixel region through priori knowledge, and each superpixel region is divided, so that candidate bacterium regions are determined; feature extraction is conducted on the candidate bacterium regions; extracted features are compared with classification standards in the classifier, and classification is completed according to similarity. The invention further provides application of the method in diagnosis of vagina bacteria. According to the bacterium division and classification method, division is conducted through calculation of the superpixels, classification is conducted through in-depth learning, and therefore the bacterium division and classification method has the advantages that the identification degree is high, cost is low, implementation is simple, and popularization is easy.

Description

Bacterium based on super pixel and degree of depth study is cut apart and sorting technique and application thereof
Technical field
The present invention relates to a kind of image and cut apart and sorting technique, relate in particular to a kind of bacterium based on super pixel and degree of depth study and cut apart and sorting technique and the application in vaginal bacteria diagnosis thereof.
Background technology
Be modal disease among women by bacterial vaginal disease or infection (vaginal candida/trichomonad, gonococcus, Chlamydia), also cause very high mortality ratio.The classification of carrying out vaginal disease by bacteria types and counting has very important effect in clinical practice.At present, be widely used and prevent that the diagnostic method of vaginal disease from being cytology examination, this kind of method depends on clinician's experience to a great extent, obtains diagnostic result accurately with this.In order to address this problem, the automatic diagnostics of design and development prevents vaginal disease, and inflammation and cancer have attracted a lot of people's interest, and becomes a focus.
Previously there is a large amount of research work to cut apart nucleus, but only utilized the segmentation performance of nucleus information approach still can not be satisfactory.Nuclear dividing method is broadly divided into multiple nucleus segmentation thresholds to be chosen, Hough conversion and watershed method.But these methods are the nucleus based on normal condition, instead of there are disease or abnormal nucleus.Recently, also having to cut apart has pathology and normal cell, and the report of cutting apart of cell mixing.
As Yeoman, C.J., Thomas, S.M., Miller, M.E.B., Ulanov, A.V., Torralba, M., Lucas, S., Gillis, M., Cregger, M., Gomez, A., Ho, M., Leigh, S.R., Stumpf, R., Creedon, D.J., Smith, M.A., Weisbaum, J.S., Nelson, K.E., Wilson, B.A., White, B.A.:A Multi-Omic Systems-Based Approach Reveals Metabolic Markers of Bacterial Vaginosis and Insight into the Disease.PLoS ONE8 (2), e56111 (2013) [1].
The work that cell splits from image, current a lot of algorithms are all based on nucleus independently, and to various kinds of cell to cut apart research less.Cut apart and can be divided into parametric filtering based on shape and marginal information nucleus, movable contour model and difference maximize.In addition, cut apart work and also obtained because merging previous knowledge and local feature the performance showing.
Therefore, how to design a kind of bacterium based on super pixel and degree of depth study and cut apart and sorting technique and application thereof, become new R&D direction.
Summary of the invention
The present invention is directed to this problem, provide a kind of bacterium based on super pixel and degree of depth study to cut apart and sorting technique and application thereof.
Bacterium based on super pixel and degree of depth study provided by the invention is cut apart and sorting technique, comprises by training plan image set and sets up degree of deep learning classification device, and test pattern and degree of deep learning classification device are contrasted to the result of output category; The process of described contrast comprises: described test pattern is done to medium filtering through each GRB passage, and remove noise; Calculate super pixel; Calculate color, shape, the size characteristic of each super pixel region; Utilize priori to carry out preliminary filtering to each super pixel region, and cut apart to determine candidate bacterium region; Feature extraction is carried out in described candidate bacterium region; Criteria for classification in the feature of extraction and described sorter is contrasted, complete classification according to similarity.
Preferably, the described step of setting up degree of deep learning classification device comprises: initialization convolutional neural networks; Receive the image pattern from described training plan image set; Actual output is calculated in forward transmission; Calculate the poor of actual output and target output; Utilize the backpropagation of minimization error approach to adjust weights; Judge whether the frequency of training that reaches predetermined; If do not reached, continue and receive above-mentioned image pattern, and adjust weights; If reached, output category standard, and deposit in described degree of deep learning classification device.
Preferably, the super pixel of described calculating is the algorithm that adopts linear iteration cluster.
Vaginal bacteria based on super pixel and degree of depth study provided by the invention is cut apart and categorizing system, comprising: training plan image set, for storing the sample image of vaginal bacteria; Degree of deep learning classification device, for storing the criteria for classification arriving based on described training plan image set gained; Pretreatment module, for test pattern is carried out to pre-service, calculate super pixel and calculate color, shape, the size characteristic of each super pixel region, utilize priori to carry out preliminary filtering to each super pixel region, and cut apart to determine candidate bacterium region; Characteristic extracting module, for carrying out feature extraction to described candidate bacterium region; Judge module, for the criteria for classification of the feature of extraction and described degree of deep learning classification device is contrasted, completes classification according to similarity.
Preferably, described degree of deep learning classification device also comprises: initialization module, for initialization convolutional neural networks; Receiver module, for receiving the image pattern from described training plan image set; Adjusting module, for calculating actual output to transmitting, calculating actual output with the poor of target output and utilize the backpropagation of minimization error approach to adjust weights; Counting module, for the frequency of training that judges whether to reach predetermined, and after reaching, notice adjusting module output category standard.
Preferably, the super pixel of described calculating is the algorithm that adopts linear iteration cluster.
Bacterium based on super pixel and degree of depth study of the present invention is cut apart and sorting technique and application thereof, is calculated and is cut apart and learn to classify by the degree of depth by super pixel, has advantages of high identification, low cost, the simple and easy popularization of enforcement.
Brief description of the drawings
Fig. 1 is the schematic flow sheet of setting up the method for degree of deep learning classification device in the present invention.
Fig. 2 is that the bacterium that the present invention is based on the study of super pixel and the degree of depth is cut apart and the schematic flow sheet of sorting technique.
Fig. 3 is that the bacterium that the present invention is based on the study of super pixel and the degree of depth is cut apart and the structural representation of categorizing system.
Fig. 4 is the schematic diagram of medial vagina common bacteria of the present invention.
Fig. 5 is calculating and the effect schematic diagram of cutting apart of carrying out and feature extraction based on super pixel in the present invention.
Fig. 6 is typical vagina image and the result to vaginal bacteria segmentation and classification in the present invention.
Fig. 7 is the exemplary plot of segmentation effect in the present invention.
Fig. 8 is the exemplary plot of cutting apart comparative result in the present invention.
Fig. 9 is the classification results comparative example figure of different sorters in the present invention.
Embodiment
The invention provides a kind of bacterium based on super pixel and degree of depth study cuts apart and sorting technique, can be applicable to identification and the classification of each bacterioid, there is the advantages such as quick, accurate, with low cost, idiographic flow refers to embodiment 1, the application of said method in the diagnosis of vaginal bacteria is also provided, and concrete system architecture refers to embodiment 2.
Embodiment 1
Incorporated by reference to Fig. 1 and Fig. 2, shown in, for the bacterium based on super pixel and degree of depth study in the present invention is cut apart and sorting technique.Mainly comprise the following steps:
One, set up degree of deep learning classification device by training plan image set;
Two, test pattern and degree of deep learning classification device are contrasted to the result of output category.
Refer to Fig. 1, be depicted as the step of setting up degree of deep learning classification device, specifically comprise:
In step S101, initialization convolutional neural networks.
In step S102, receive the image pattern from described training plan image set.
In step S103, actual output is calculated in forward transmission.
In step S104, calculate the poor of actual output and target output.
In step S105, utilize the backpropagation of minimization error approach to adjust weights.
In step S106, judge whether the frequency of training that reaches predetermined.
If do not reached, return to step S102 and continue and receive above-mentioned image pattern, and adjust weights.
If reached, in step S107, output category standard and priori, and deposit in described degree of deep learning classification device.
Refer to Fig. 2, be depicted as bacterium based on the study of super pixel and the degree of depth and cut apart and the process flow diagram of sorting technique, what this figure more stressed is the contrast step of test pattern, comprising:
In step S201, described test pattern is done to medium filtering through each GRB passage, and remove noise.
In step S202, calculate super pixel.
Because super pixel algorithm is very compact and feature flexibly, and the atomic region pixel with perception meaning can be flocked together, therefore, be applied in computer aided calculation and can reduce costs and labour.
In step S203, calculate color, shape, the size characteristic of each super pixel region.
In step S204, utilize priori to carry out preliminary filtering to each super pixel region, and cut apart to determine candidate bacterium region.
Wherein, priori, comprise: the numerical value upper and lower limit of the each RGB passage in bacterium region, the upper and lower limit of bacterium length and width, the upper and lower limit of bacterium field color average, the upper and lower limit of bacterium area, girth, a rough estimates value of namely by degree of deep learning classification table, enough samples being done.
In step S205, feature extraction is carried out in described candidate bacterium region.
In step S206, the criteria for classification in the feature of extraction and described sorter is contrasted.
In step S207, complete classification according to similarity.
Similarity, the namely score of the feature of candidate region after the criteria for classification of sorter contrasts, the numerical value of the test mark of gained and the label of affiliated bacteria types is more close, is considered to similarity higher, just this test zone is classified as to the bacterium that changes type.
In other embodiments, when similarity is during lower than certain predetermined threshold value, according to the needs of the state of an illness or pathology, the too low candidate region of similarity is abandoned or paid close attention to.
Bacterium based on super pixel and degree of depth study of the present invention is cut apart and sorting technique, is calculated and is cut apart and learn to classify by the degree of depth by super pixel, has advantages of high identification, low cost, the simple and easy popularization of enforcement.
Embodiment 2
Refer to Fig. 3, be depicted as a kind of vaginal bacteria based on super pixel and degree of depth study in the present invention and cut apart and categorizing system.Described system comprises training plan image set 10, degree of deep learning classification device 20, pretreatment module 30, characteristic extracting module 40 and judge module 50.
Training plan image set 10, for storing the sample image of vaginal bacteria.
Degree of deep learning classification device 20, for storing the criteria for classification arriving based on described training plan image set gained.
In the present embodiment, described degree of deep learning classification device 20, also comprises: initialization module 21, for initialization convolutional neural networks; Receiver module 22, for receiving the image pattern from described training plan image set 10; Adjusting module 23, calculates actual output, calculates actual output with the poor of target output and utilize the backpropagation of minimization error approach to adjust weights for forward transmission; Counting module 24, for the frequency of training that judges whether to reach predetermined, and after reaching, notice adjusting module 23 output category standards.
Refer to Fig. 4, be depicted as the description of the criteria for classification of vaginal bacteria.Learn from practice, vaginal bacteria is divided into Four types: comprise positive bacillus, negative bacillus, positive coccus and negative cocci.
From color differentiating: positive be generally blue, negative general pinkiness;
Distinguish from shape: bacillus is generally shaft-like, it is spherical that coccus is generally, but in overlapping situation, have different forms;
Distinguish from area: positive bacillus is substantially all greater than 250, negative and positive bacillus is substantially all greater than 150 but be slightly smaller than positively, and the area of positive coccus and negative cocci is generally all less than 200.
In addition, degree of deep learning classification device 20, also calculates and stores priori for being in course of adjustment, comprise: the numerical value upper and lower limit of the each RGB passage in bacterium region, the upper and lower limit of bacterium length and width, the upper and lower limit of bacterium field color average, the upper and lower limit of bacterium area, girth.
Pretreatment module 30, for test pattern is carried out to pre-service, calculate super pixel and calculate color, shape, the size characteristic of each super pixel region, utilize priori to carry out preliminary filtering to each super pixel region, and cut apart to determine candidate bacterium region.
Wherein, calculate super pixel, can utilize the algorithm of the super pixel of simple linear iteration cluster (SLIC), for bacterium can provide good border.The feature that SLIC algorithm has simply, remembers fast and efficiently, can reduce complicacy and raising speed by a pre-treatment step.And there is cluster advantage and superperformance, be applicable to very much cutting apart bacterium.Characteristic extracting module 40, for carrying out feature extraction to described candidate bacterium region.
Refer to Fig. 5, be depicted as that pretreatment module and characteristic extracting module are calculated based on super pixel and the design sketch of cutting apart of carrying out and feature extraction.Eigenwert resolving power in Fig. 5 is higher, can isolate fast coccus and bacillus.The border of each super pixel has real image boundary and is closely related.And because the border of image is retained, the method for super pixel is very effective to cutting apart, and ensure the accuracy of its follow-up extraction.
Judge module 50, for the criteria for classification of the feature of extraction and described degree of deep learning classification device is contrasted, completes classification according to similarity.
Similarity, the namely score of the feature of candidate region after the criteria for classification of sorter contrasts, the numerical value of the test mark of gained and the label of affiliated bacteria types is more close, is considered to similarity higher, just this test zone is classified as to the bacterium that changes type.
In other embodiments, when similarity is during lower than certain predetermined threshold value, according to the needs of the state of an illness or pathology, the too low candidate region of similarity is abandoned or paid close attention to.
Experimental result
One, material and data
From South Mountain, Shenzhen hospital, to the women of 18 to 50 years old, 105 slides are collected altogether for the collection of vaginal cell data.Then use Olympus BX43 microscope, it is (oily mirror under the condition of 100 times at objective lens magnification, its numerical aperture is 1.25), each slide is at least gathered to 105 reasonable visuals field as deal with data, the rgb image of the jpg that the picture obtaining is 1360*1024.Obtain after raw data, under doctor's guidance, the picture often running at work taking doctor is standard, has chosen altogether the test picture of 319 pictures as algorithm.
Two, segmentation result
The popular approach of the assessment to system performance is all used as accuracy rate, recall rate, degree of accuracy, sensitivity, specificity, F1 estimate with Zijdenbos index of similarity (ZSI) etc.In 6 kinds of typical cell images, identification different bacterium manually and automatic segmentation result more as shown in Figure 6.As can be seen from Figure 6, based on the manual operations of doctors experience, the effect of auto Segmentation is also very good.Quantitative test for segmentation result shows at Fig. 7.Segmentation performance is very good as can be seen from Figure 7.Fig. 8 has listed the comparison on the distinct methods in segmentation result.We can see, the segmentation result proposing is better than partitioning algorithm used in background technology [1].
Three, classification results
Utilize different sorters as degree of depth study (CNN), reverse transmittance nerve network (BNN), probabilistic neural network (PNN), support vector machine (SVM) and learn vector quantization (LVQ) vaginal cell is classified, and carrying out Performance Ratio.BNN is the sorting technique based on supervision, and the method is adjusted the weight of each layer by using gradient to minimize objective function.
Fig. 9 has summed up the performance of the sorter different based on representational feature.Can find out from the result that Fig. 9 is quantitative, the sorting technique of CNN is better than other sorting techniques, and the method that has simultaneously shown degree of depth study is the method for very effective vaginal bacteria classification.But due to its limited network layer, the result of BNN is quite poor.Obviously, enough high to the classification performance of vaginal bacteria.As can be seen from the results, the classification of vaginal cell meets the requirement using in real life.
Four, conclusion
Herein to super pixel and the application of dark learning art and vaginal cell cut apart and classification is studied, utilize these two kinds of technology that vaginal bacteria is divided into four classes.Experimental result shows, the algorithm of super pixel segmentation is most suitable to cutting apart of vaginal bacteria, has obtained the effect of highly significant.Based on the super pixel tag of degree of deep learning training, and vaginal bacteria is identified, also obtained extraordinary Classification and Identification result.The algorithm proposing has obtained the effect of significantly cutting apart and classify and has shown, vaginal bacteria automatic classification and identification contribute to doctor's diagnosis, and accuracy rate is high.
The above is only the preferred embodiment of the present invention; it should be pointed out that for those skilled in the art, under the premise without departing from the principles of the invention; can also make some improvements and modifications, these improvements and modifications also should be considered as protection scope of the present invention.

Claims (8)

1. the bacterium based on super pixel and degree of depth study is cut apart and a sorting technique, comprises by training plan image set and sets up degree of deep learning classification device, and test pattern and described degree of deep learning classification device are contrasted to the result of output category; It is characterized in that: the process of described contrast comprises:
Described test pattern is done to medium filtering through each GRB passage, and remove noise;
Calculate super pixel;
Calculate color, shape, the size characteristic of each super pixel region;
Utilize priori to carry out preliminary filtering to described each super pixel region, and cut apart to determine candidate bacterium region;
Feature extraction is carried out in described candidate bacterium region;
Criteria for classification in the feature of extraction and described degree of deep learning classification device is contrasted;
Export the result of described classification according to similarity.
2. bacterium as claimed in claim 1 is cut apart and sorting technique, it is characterized in that, the described step of setting up degree of deep learning classification device comprises:
Initialization convolutional neural networks;
Receive the image pattern from described training plan image set;
Actual output is calculated in forward transmission;
Calculate the poor of actual output and target output;
Utilize the backpropagation of minimization error approach to adjust weights;
Judge whether the frequency of training that reaches predetermined;
If do not reached, continue and receive above-mentioned image pattern, and adjust weights;
If reached, export described criteria for classification, and deposit in described degree of deep learning classification device.
3. bacterium as claimed in claim 1 is cut apart and sorting technique, it is characterized in that, the super pixel of described calculating is the algorithm that adopts linear iteration cluster.
4. bacterium as claimed in claim 1 is cut apart and sorting technique, it is characterized in that, when described similarity is during lower than predetermined threshold value, abandons or pay close attention to its corresponding candidate bacterium region.
5. the vaginal bacteria based on super pixel and degree of depth study is cut apart and a categorizing system, it is characterized in that, comprising:
Training plan image set, for storing the sample image of vaginal bacteria;
Degree of deep learning classification device, for storing the criteria for classification arriving based on described training plan image set gained;
Pretreatment module, for test pattern is carried out to pre-service, calculate super pixel and calculate color, shape, the size characteristic of each super pixel region, utilize priori to carry out preliminary filtering to each super pixel region, and cut apart to determine candidate bacterium region;
Characteristic extracting module, for carrying out feature extraction to described candidate bacterium region;
Judge module, for the criteria for classification of the feature of extraction and described degree of deep learning classification device is contrasted, completes classification according to similarity.
6. vaginal bacteria as claimed in claim 5 is cut apart and categorizing system, it is characterized in that, described degree of deep learning classification device also comprises:
Initialization module, for initialization convolutional neural networks;
Receiver module, for receiving the image pattern from described training plan image set;
Adjusting module, calculates actual output, calculates actual output with the poor of target output and utilize the backpropagation of minimization error approach to adjust weights for forward transmission;
Counting module, for the frequency of training that judges whether to reach predetermined, and after reaching, notice adjusting module output category standard.
7. vaginal bacteria as claimed in claim 5 is cut apart and categorizing system, it is characterized in that, the super pixel of described calculating is the algorithm that adopts linear iteration cluster.
8. vaginal bacteria as claimed in claim 5 is cut apart and sorting technique, it is characterized in that, when described similarity is during lower than predetermined threshold value, abandons or pay close attention to its corresponding candidate bacterium region.
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