NL2027491A - Method for rapidly identifying identities of pumpkin seeds - Google Patents

Method for rapidly identifying identities of pumpkin seeds Download PDF

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NL2027491A
NL2027491A NL2027491A NL2027491A NL2027491A NL 2027491 A NL2027491 A NL 2027491A NL 2027491 A NL2027491 A NL 2027491A NL 2027491 A NL2027491 A NL 2027491A NL 2027491 A NL2027491 A NL 2027491A
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thz
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Bao Yidan
Feng Xuping
Mi Chunxiao
He Yong
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Univ Zhejiang
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Abstract

The present disclosure discloses a method for rapidly identifying identities of pumpkin seeds and belongs to the technical field of phenotype acquisition in crop breeding. The method includes: keeping pumpkin seeds of all varieties indoors at a constant temperature and a constant humidity; using terahertz (THZ) pulses to acquire THz image signals of pumpkin samples and deriving original THz spectroscopic time-domain transform spectral lines; where, the spectral line is denoted as X and a variety of pumpkin in the sample is denoted as Y; according to the original THz spectroscopic time-domain transform spectral line X, finding a characteristic frequency domain value corresponding to a pumpkin; extracting THz spectroscopic refractive index data corresponding to the characteristic frequency domain value of pumpkin from X, which are denoted as X1, and dividing obtained data (X1, Y) into a modeling set and a prediction set; with X1 and Y in the modeling set as input and output; respectively; building a convolutional neural network (CNN) multi-classif1cation model of pumpkin varieties and refractive indexes of corresponding THz time-domain transform spectral lines; and substituting the spectroscopic refractive index X1 of a pumpkin in the prediction set into the CNN multi-classif1cation model to obtain a corresponding variety of the pumpkin to be tested.

Description

METHOD FOR RAPIDLY IDENTIFYING IDENTITIES OF PUMPKIN SEEDS The present disclosure relates to the technical field of phenotype acquisition in crop breeding, and in particular to a method for rapidly identifying identities of pumpkin seeds.
Pumpkin is a healthy vegetable with high nutritional value, and has high development and utilization value and potential. Pumpkin itself has high nutritional and healthy values, and pumpkin seeds are also rich in fatty acids, amino acids, sterols, proteins, vitamins, and other trace elements, exhibiting the effects of lung nourishing, phlegm reducing, pain alleviating, diuresis, and the like. Pumpkin can resist oxidation, prevent and treat prostatic diseases, lower cholesterol, alleviate high blood pressure, prevent and relieve cardiovascular diseases. Moreover, an extract of pumpkin has the effect of expelling parasites and is also used in clinical treatment of abdominal pain and fullness and parasitic diseases. Therefore, pumpkin is a food with health care functions.
With the development of cross breeding, it is necessary to dig deeper into genetic information, so that huge breakthroughs have been made in the field of genetics. However, traditional methods for acquiring crop phenotypes in cross breeding cannot meet the requirements of the development of high-throughput sequencing technology. Therefore, there is a need for a high-throughput phenotype acquisition method that can achieve rapid determination of phenotypic information in pumpkin cross breeding.
Terahertz time-domain spectroscopy (THz-TDS) is a spectroscopic detection technique where medium information carried in broadband terahertz (THz) pulses is used to extract internal information of a material, which is often used in the field of nondestructive testing of materials. THz-TDS is one of the emerging spectroscopic detection techniques in detection research and has received extensive attention in the detection of crop phenotypes. Because the physiological and morphological information of a test sample is acquired in a non-contact and non-destructive manner, the phenotypic information of a crop can be obtained in real time, which provides a strong technical support for testing and screening in pumpkin cross breeding.
Chinese patent CN106841054A discloses a method for identifying seed varieties, including the following steps: acquiring P terahertz images of each sample seed in a test set at P bands; acquiring characteristic parameters for each sample seed according to the P terahertz images; inputting the characteristic parameters into a classification model to obtain a predicted variety for each sample seed; selecting a predetermined sample seed from the test set according to the predicted variety, and updating the classification model according to the predetermined sample 1 seed; and using an updated classification model to identify a variety of a sample seed in the test set.
When the above method is used to identify seed varieties, the classification model of resumes is unstable and cannot achieve the purpose of rapid identification.
The present disclosure is intended to provide a method for rapidly identifying identities of pumpkin seeds, which can realize the acquisition and rapid identification of pumpkin variety phenotype information in cross breeding.
To achieve the above purpose, the present disclosure provides a method for rapidly identifying identities of pumpkin seeds, including the following steps: 1) keeping pumpkin seeds of all varieties indoors at a constant temperature and a constant humidity; 2) using THz pulses to acquire THz image signals of pumpkin samples and deriving original THz spectroscopic time-domain transform spectral lines, where, the spectral line is denoted as X and a variety of pumpkin in the sample is denoted as Y; 3) according to the original THz spectroscopic time-domain transform spectral line X, finding a characteristic frequency domain value corresponding to a pumpkin; 4) extracting THz spectroscopic refractive index data corresponding to the characteristic frequency domain value of pumpkin in step 3) from X, which are denoted as X1, and dividing obtained data (X1, Y) into a modeling set and a prediction set in proportion; 5) with X1 and Y in the modeling set as input and output, respectively, building a convolutional neural network (CNN) multi-classification model of pumpkin varieties and refractive indexes of corresponding THz time-domain transform spectral lines; and 6) substituting the spectroscopic refractive index X1 of a pumpkin in the prediction set into the CNN multi-classification model to obtain a corresponding variety of the pumpkin to be tested.
In the above technical solution, the rapid identification of identities of pumpkin seeds is realized, which has the characteristics of simple operation, low detection cost, high-throughput acquisition, and high accuracy, and effectively overcomes the shortcomings of the traditional methods for acquiring and detecting phenotypic information in breeding, such as complex operation, high cost, and large damage to samples.
Preferably, in step 1), all pumpkin seeds may be kept in a kraft paper bag under the same external conditions, and only the variety is set as a variable.
Preferably, in step 2), the original THz spectroscopic time-domain transform spectral line may be obtained by subjecting time-domain spectroscopic information obtained by a THz 2 time-domain spectrometer and sample thickness data to Fourier transform (FT).
Preferably, in step 2), parameters of a signal acquisition system may be optimized, and optimized parameters may be as follows: 1,560 nm femtosecond laser, and 780 nm femtosecond pulse with a bandwidth of 100 fs.
Preferably, in step 5), the CNN multi-classification model may include five modules of input layer, convolutional layer, pooling layer, fully connected layer, and output layer; the convolution module may have five layers, consisting of five convolutional layers and five max-pooling layers, with convolutional kernels of 3 x 3; the number of filters may decrease sequentially from 256; the max-pooling may adopt 2 x 2; there may be three fully connected layers; the number of neural nodes may decrease sequentially from 512; during an identification process, a neuronal activation function of elu may be always used; and finally, at the output layer, a multi-classification activation function of softmax may be used to obtain an output of pumpkin variety.
Preferably, the CNN deep learning mode may explore more representative characteristic information of a pumpkin THz spectrum layer by layer through the convolutional layers and the fully connected layers; an optimization algorithm may be introduced to generate more accurate weight and bias values; and the optimization algorithm may adopt SGD learning rate: 1r0.01, momentum parameter: momentum0.9, and learning rate attenuation value for each update: 0.
In order to prevent over-fitting, preferably, Batch Normalization may be added to the convolution module to improve the generalization ability of the model, which is located after the convolutional layer and before the max-pooling.
Compared with the prior art, the present disclosure has the following beneficial effects.
(1) The method for rapidly identifying identities of pumpkin seeds according to the present disclosure realizes the rapid identification of pumpkin seed varieties, which is beneficial to the development of portable sensing instruments for pumpkin seeds in cross breeding.
(2) The present disclosure utilizes a variety identification detection method based on a THz-TDS imaging technology, which effectively overcomes the disadvantages of traditional detection methods such as complicated procedures, high cost, and large damage to samples, and shows the characteristics of simple operation, low cost, fast, efficient and accurate detection, or the like.
FIG. 1 is a schematic structural diagram of a CNN for deep learning in an example of the present disclosure.
3
To make the objectives, technical solutions, and advantages of the present disclosure clearer, the present disclosure is further described below with reference to examples and accompanying drawings.
Example In this example, a method for rapidly identifying identities of pumpkin seeds included the following steps: Step S1: Samples were collected and stored. The pumpkin seed samples used in this example were provided by the Zhejiang Academy of Agricultural Sciences. The experimental subjects included 76 genotypes of pumpkin seed samples, namely, toad pumpkin, wheat cake ornamental gourd, Torreva grandis ornamental gourd, calabash ornamental gourd, landmine pumpkin, Dongyang old variety ornamental gourd, old ornamental gourd, Chengxi pumpkin, hard pumpkin, Wenling local pumpkin, high lamp squash, millet squash, large-petal squash, long squash, round squash, broad-seed summer pumpkin, long-stalked autumn pumpkin, round pumpkin, charcoal squash, jatropha squash, brushed skin pumpkin, tower ten sisters, powdery pumpkin, local round pumpkin, local pumpkin, coastal pumpkin, Putan pumpkin, Cha Kengtu pumpkin, old pumpkin, long leprosy pumpkin, leprosy pumpkin, pear-shaped pumpkin, flat pumpkin, lump pumpkin, golden wire squash, round pumpkin, Changtong pumpkin, Mapi pumpkin, 4 kinds of pockmarked pumpkin, 2 kinds of long pumpkin, 4 kinds of indigenous pumpkins, 14 kinds of ornamental gourds, and 21 kinds of other pumpkins. The pumpkin seed were all kept in a kraft paper bag and placed in a greenhouse with a constant temperature and humidity.
Step S2: THz imaging spectrum signals of the samples were acquired. A THz instrument was adjusted to the state of projection imaging module, and nitrogen was charged into a test chamber thereof for 30 min until the signal was stable, thus avoiding the influence of moisture as much as possible. A scotch tape was first pasted on a sample holder and placed in the test room to acquire a THz signal of the tape as a background signal; then pumpkin samples were fixed on the sample holder with the scotch tape and placed in the test room; THz imaging signals were acquired; and original THz spectroscopic time-domain transform spectral lines were derived. The spectral line was denoted as X and a variety of pumpkin in the sample was denoted as Y.
Step S3: According to the original THz spectroscopic time-domain transform spectral line X, a frequency domain value of the characteristic spectral line corresponding to main characteristics of a pumpkin.
Step S4: THz spectroscopic refractive index data corresponding to the characteristic frequency domain value of pumpkin in step 3) were extracted from X, which were denoted as X1, and obtained data (X1, Y) were divided into 5,000 modeling set samples and 2,500 prediction set 4 samples in a ratio of 2:1.
Step S5: With X1 and Y in the modeling set as input and output, respectively, a CNN multi-classification model of pumpkin varieties and refractive indexes of corresponding THz time-domain transform spectral lines was built.
Step S6: The spectroscopic refractive index Xl of a pumpkin in the prediction set was substituted into the CNN multi-classification model to obtain a corresponding variety of the pumpkin to be tested.
As shown in FIG. I, in this example, the CNN multi-classification model included five modules of input layer, convolutional layer, pooling layer, fully connected layer, and output layer; the convolution module had five layers, consisting of five convolutional layers and five max-pooling layers, with convolutional kernels of 3 x 3; the number of filters decreased sequentially from 256; the max-pooling adopted 2 * 2; in order to prevent over-fitting, Batch Normalization was added to a position after the convolutional layer and before the max-pooling, thus improving the generalization ability of the model; there were three fully connected layers; the number of neural nodes decreased sequentially from 512; during an identification process, a neuronal activation function of elu was always used; and finally, at the output layer, a multi-classification activation function of softmax was used to obtain an output of pumpkin variety.
In this example, the CNN deep learning mode explored more representative characteristic information of a pumpkin THz spectrum layer by layer through the convolutional layers and the fully connected layers; an optimization algorithm was introduced to generate more accurate weight and bias values; and the optimization algorithm adopted SGD parameters: learning rate: 1r0.01, momentum=0.9, and nesterov=False. This model was built using the third-party library keras in python 3. Results showed that an actual pumpkin variety was in excellent agreement with a variety corresponding to a THz time-domain transform spectrum predicted by the CNN model, with an accuracy of the prediction set reaching 94%.
The above results indicate that the method of the present disclosure can realize the rapid identification of pumpkin seed identities and has a promising application prospect.
5

Claims (7)

Conclusies I. Werkwijze voor het snel identificeren van identiteiten van pompoenzaden, omvattende de volgende stappen: 1) het binnen houden van pompoenzaden van alle variéteiten op een constante temperatuur en met een constante vochtigheid; 2) het gebruik maken van terahertz (THz) golven om THz beeldsignalen van pompoenmonsters te verkrijgen en het afleiden van originele THz spectroscopische tijdsdomein transformatie spectraallijnen, waarbij, de spectraallijn wordt aangegeven als X en een variëteit van pompoen in het monster wordt aangegeven als Y; 3) volgens de originele THz spectroscopische tijdsdomein transformatie spectraallijn X, het vinden van een karakteristieke frequentiedomeinwaarde overeenkomstig een pompoen; 4) het extraheren van THz spectroscopische refractieve indexdata overeenkomstig de karakteristieke frequentiedomeinwaarde van een pompoen in stap 3) van X, die wordt aangegeven met Xi, en het verdelen van de verkregen gegevens (X1, Y) in een modelleerset en een voorspellingsset in proportie; 5) met X1 en Y in de modelleerset als invoer en uitvoer, respectievelijk, het bouwen van een convolutioneel neuraal netwerk (CNN) multiclassificatie model van pompoenvariaties en refractieve indexen van overeenkomstige THz tijdsdomein transformatie spectraallijnen; en 6) het vervangen van de spectroscopische refractieve index X1 van een pompoen in de voorspellingsset in het CNN multiclassificatie model om een overeenkomstige variëteit van de te testen pompoen te verkrijgen.Claims I. A method of rapidly identifying pumpkin seed identities comprising the steps of: 1) keeping pumpkin seeds of all varieties indoors at a constant temperature and humidity; 2) using terahertz (THz) waves to obtain THz image signals from pumpkin samples and derive original THz spectroscopic time domain transformation spectral lines, wherein the spectral line is indicated as X and a variety of pumpkin in the sample is indicated as Y; 3) according to the original THz spectroscopic time domain transform spectral line X, finding a characteristic frequency domain value corresponding to a pumpkin; 4) extracting THz spectroscopic refractive index data according to the characteristic frequency domain value of a pumpkin in step 3) from X, denoted by Xi, and dividing the obtained data (X1, Y) into a modeling set and a prediction set in proportion; 5) using X1 and Y in the modeling set as inputs and outputs, respectively, building a convolutional neural network (CNN) multiclassification model of pumpkin variations and refractive indices of corresponding THz time domain transform spectral lines; and 6) replacing the spectroscopic refractive index X1 of a pumpkin in the prediction set in the CNN multiclassification model to obtain a corresponding variety of the pumpkin to be tested. 2. Werkwijze voor het snel identificeren van identiteiten van pompoenzaden volgens conclusie 1, waarbij, in stap 1), alle pompoenzaden worden bewaard in een kraft papieren zak onder dezelfde externe omstandigheden, en alleen de variëteit is ingesteld als een variabele.The method for rapidly identifying pumpkin seed identities according to claim 1, wherein, in step 1), all pumpkin seeds are stored in a kraft paper bag under the same external conditions, and only the variety is set as a variable. 3. Werkwijze voor het snel identificeren van identiteiten van pompoenzaden volgens conclusie 1, waarbij in stap 2), de originele THz spectroscopische tijdsdomein transformatie spectraallijn wordt verkregen door het onderwerpen van een tijdsdomein spectroscopische informatie verkregen door een THz tijdsdomein spectrometer en monsterdikte gegevens aan Fourier transformatie (FT).The method for rapidly identifying pumpkin seed identities according to claim 1, wherein in step 2), the original THz spectroscopic time domain transform spectral line is obtained by subjecting a time domain spectroscopic information obtained by a THz time domain spectrometer and sample thickness data to Fourier transform. (FT). 4. Werkwijze voor het snel identificeren van identiteiten van pompoenzaden volgens conclusie 1, waarbij in stap 2), parameters van een signaalacquisitiesysteem wordt geoptimaliseerd, en geoptimaliseerde parameters zijn als volgt: 1560 nm femtoseconde laser, en 780 nm femtoseconde puls met een bandbreedte van 100 fs.The method for rapidly identifying pumpkin seed identities according to claim 1, wherein in step 2), parameters of a signal acquisition system are optimized, and optimized parameters are as follows: 1560 nm femtosecond laser, and 780 nm femtosecond pulse with a bandwidth of 100 fs. 5. Werkwijze voor het snel identificeren van identiteiten van pompoenzaden volgens conclusie 1, waarbij in stap 5), het CNN multiclassificatiemodel vijf modulen omvat van een invoerlaag, een convolutionele laag, een samenkomstlaag, volledig verbonden laag, een uitvoerlaag; de convolutiemodule heeft vijf lagen, bestaande uit vijf convolutionele lagen en vijf max-samenkomstlagen, met convolutionele kernels van 3x3; het aantal filters vermindert opeenvolgend van 256; de max-samenkomst neemt 2x2 aan; er zijn drie volledig verbonden lagen, het aantal neurale knopen vermindert opeenvolgend van 512; tijdens een identificatieproces, wordt altijd een neuronale activatiefunctie van elu gebruikt; en tot slot, bij de uitvoerlaag, wordt een multi-classificatie activatiefunctie van softmax gebruikt om een uitvoer van pompoen variëteit te verkrijgen.The method for rapidly identifying pumpkin seed identities according to claim 1, wherein in step 5), the CNN multiclassification model comprises five modules of an input layer, a convolutional layer, a convergence layer, fully connected layer, an output layer; the convolution module has five layers, consisting of five convolutional layers and five max convergence layers, with 3x3 convolutional kernels; the number of filters decreases sequentially from 256; the max convergence assumes 2x2; there are three fully connected layers, the number of neural nodes decreases sequentially from 512; during an identification process, a neuronal activation function of elu is always used; and finally, at the output layer, a multi-classification activation function of softmax is used to obtain a pumpkin variety output. 6. Werkwijze voor het snel identificeren van identiteiten van pompoenzaden volgens conclusie 5, waarbij de CNN diepleermodus meer representatieve karakteristieke informatie van een pompoen THz spectrum laag voor laag door de convolutionele lagen en de volledig verbonden lagen onderzoekt; een optimalisatie algoritme wordt geïntroduceerd om meer accurate gewichts- en biaswaarden te genereren; en het optimalisatie algoritme neem SGD leer verhouding aan: 110,01,The method of rapidly identifying pumpkin seed identities according to claim 5, wherein the CNN deep learning mode examines more representative characteristic information of a pumpkin THz spectrum layer by layer through the convolutional layers and the fully connected layers; an optimization algorithm is introduced to generate more accurate weight and bias values; and the optimization algorithm adopts SGD learning ratio: 110.01, momentum parameter; momentumo,9, en leer verhouding verzwakking waarde voor elke update: 0.momentum parameter; momentumo,9, and learn ratio attenuation value for each update: 0. 7. Werkwijze voor het snel identificeren van identiteiten van pompoenzaden volgens conclusie 5, waarbij Batch Normalisatie wordt toegevoegd aan de convolutiemodule, die is gelegen na de convolutionele laag en voor de max- samenkomst.The method for rapidly identifying pumpkin seed identities according to claim 5, wherein Batch Normalization is added to the convolution module located after the convolutional layer and before the max convergence.
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