MatLab Lung Segmentation: 5 Kauj Ruam

2024 Tus sau: John Day | [email protected]. Kawg hloov kho: 2024-01-30 09:24

Los ntawm: Phuc Lam, Paul Yeung, Eric Reyes

Kev lees paub tias qhov ua tsis raug ntawm lub ntsws ua segmentation yuav ua rau muaj cov ntaub ntawv tsis raug hais txog kev txheeb xyuas thaj tsam ntawm tus kab mob thiab tuaj yeem cuam tshuam ncaj qha rau cov txheej txheem kuaj mob. Cov txheej txheem pab khoos phis tawj niaj hnub ua tsis tiav los muab cov txiaj ntsig raug thaum cov kab mob hauv lub ntsws muaj cov duab nyuaj. Cov duab tsis txawv txav no tuaj yeem tshwm sim los ntawm pleural effusions, kev sib sau ua ke, thiab lwm yam. Ua ntawv thov cov txheej txheem ntsws sib cais, uas ib puag ncig ntawm lub ntsws raug cais los ntawm cov ntaub so ntswg ib puag ncig, peb lub app tuaj yeem txheeb xyuas thaj tsam nrog tus neeg siv cov tswv yim nkag los muab kev pom zoo ntawm cov duab ntawm lub ntsws, Lub hom phiaj ntawm MatLab txoj haujlwm no yog txhawm rau tsim cov neeg siv-phooj ywg sib tham sib lub ntsws app txhawm rau txheeb xyuas cov kab mob ntawm lub ntsws 'X-ray duab. Peb lub hom phiaj yog los tsim txoj hauv kev muaj txiaj ntsig zoo los qhia thiab txheeb xyuas lub ntsws tsis txawv txav txhawm rau muab cov kws kho mob thiab kws tshaj lij hluav taws xob txoj hauv kev ntseeg tau ntau dua los kuaj xyuas kab mob ntsws. Siv cov cuab yeej tsim qauv app hauv MatLab, txoj haujlwm tau tsim los ua haujlwm tshwj xeeb nrog xoo hluav taws xob hauv siab thiab suav tomography (CT) ntsuas, tab sis nws tseem tau sim ua haujlwm nrog MRI scan.

Cov lus qhia hauv qab no suav nrog peb cov txheej txheem lim suab nrov (qis-dhau Wiener lim) nrog rau cov duab pib (los ntawm kev siv qhov hnyav siv histogram ntawm cov duab grayscale) thiab siv morphological gradient (qhov sib txawv ntawm qhov nthuav dav thiab yaig ntawm cov duab) txheeb xyuas thaj tsam ntawm kev txaus siab. Cov lus qhia yuav piav qhia yuav ua li cas peb koom ua ke tag nrho cov ntsiab lus rau hauv cov duab siv interface (GUI).

Nco tseg:

1). Txoj haujlwm no tau tshoov siab los ntawm cov ntawv tshawb fawb: "Segmentation and Image Analysis of Abnormal Lungs at CT: Tam sim no mus kom ze, Teeb meem, thiab yav tom ntej tiam sis". Uas tuaj yeem pom ntawm no

2). Peb siv X-ray duab los ntawm NIH: Chaw Kho Mob. Qhov txuas tuaj yeem pom ntawm no

3). App designer pab tuaj yeem nrhiav tau ntawm no

4). Ua ntej siv txoj cai: koj yuav tsum hloov Dir path (kab 34) rau koj cov ntawv teev npe thiab hom duab (kab 35) (peb txheeb xyuas *.png).

Kauj Ruam 1: Kauj Ruam 1: Thauj Duab

Cov kauj ruam no yuav qhia koj thawj daim duab hauv cov nplai grey. Hloov 'name_of_picture.png' rau koj lub npe duab

meej; clc; kaw tag nrho;

%% Chaw thau khoom duab

raw_x_ray = 'name_of_picture.png';

Kuv = imread (raw_x_ray);

daim duab (101);

imshow (kuv);

colormap (txho);

lub npe ('Grayscale X-Ray');

Kauj Ruam 2: Kauj Ruam 2: Qhib Lub Suab nrov thiab Histogram

Txhawm rau txhawm rau nrhiav qhov pib rau cov duab teev cov xim grey, peb saib ntawm qhov histogram kom pom tias muaj cov qauv sib txawv. Nyeem ntxiv ntawm no

Kuv = wiener2 (kuv, [5 5]);

daim duab (102);

subplot (2, 1, 1);

imshow (kuv);

subplot (2, 1, 2);

imhist (kuv, 256);

Kauj Ruam 3: Kauj Ruam 3: Teem Thresholds

Cov kauj ruam no tso cai rau koj teeb tsa lub chaw pib raws li qhov histogram. morphologicalGradient yuav hais txog thaj tsam ntawm kev txaus siab rau liab, thiab kev ua haujlwm visboundaries hla cov kab lus piav qhia thiab lim ntawm lub ntsws liab.

Los ntawm kev siv thaj tsam thaj tsam, peb tuaj yeem qhia meej cov arrays ntawm kev ua tau zoo thiab txheeb lawv hauv qis. Tom ntej no kuv binarize cov duab sclae grey thiab siv morphlogical gradient method thiab mLoren Shurasking los qhia txog thaj tsam ntawm kev txaus siab (ROI). Cov kauj ruam tom ntej yog thim cov duab kom lub ntsws ROI dawb nyob rau tom qab dub. Kuv siv txoj haujlwm showMaskAsOverlay los tso saib 2 daim npog ntsej muag. Nco tseg: cov cai tau tshoov siab los ntawm Loren Shure, txuas.

Lasly, kuv tsim cov qauv xim liab los ntawm kev siv bwbwboundaries thiab npog daim duab lim thiab ciam teb.

a_thresh = Kuv> = 172; % teeb tsa qhov pib no

[labelImage, numberOfBlobs] = bwlabel (a_thresh);

khoom siv = thaj tsam cov khoom siv (a_thresh, 'tag nrho');

sortedSolidity = txheeb ([props. Solidity], 'nqis');

SB = sortedSolidity (1);

yog SB == 1 % SB tsuas lees txais kev sib tw == 1 lim tawm cov pob txha

binaryImage = imbinarize (kuv); daim duab (103);

imshow (binaryImage); colormap (txho);

SE = strel ('xwmfab', 3);

morphologicalGradient = imsubtract (imdilate (binaryImage, SE), imerode (binaryImage, SE));

daim npog = imbinarize (morphologicalGradient, 0.03);

SE = strel ('xwmfab', 2);

mask = imclose (mask, SE);

mask = imfill (daim npog, 'qhov');

mask = bwareafilt (daim npog, 2); % tswj tus naj npawb ntawm thaj tsam qhia

notMask = ~ daim npog;

daim npog = daim npog | bwpropfilt (notMask, 'Area', [-Inf, 5000 - eps (5000)]));

showMaskAsOverlay (0.5, daim npog, 'r'); % koj yuav tsum rub tawm app/ua haujlwm showMaskAsOverlay

BW2 = imfill (binaryImage, 'qhov');

new_image = BW2;

new_image (~ daim npog) = 0; % thim keeb kwm yav dhau thiab qhov

B = bwboundaries (tshiab_image); % tsuas tuaj yeem lees txais 2 qhov ntev

daim duab (104);

imshow (tshiab_image);

tuav

visboundaries (B);

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Kauj ruam 4: Tsim GUI

Tam sim no, peb koom ua ke cov cai ua ntej hauv MATLAB app. Qhib App Designer hauv MATLAB (Tshiab> App). Ua ntej, peb tsim lub interface los ntawm nyem-tuav-thiab rub hauv peb txoj kab mus rau hauv chaw ua haujlwm nruab nrab. Tom ntej no, peb nyem-tuav-luag ob lub nyees khawm, ib qho hloov kho kab ntawv (kab ntawv), ib qho hloov chaw (lej), ib qho swb, thiab ib daim ntawv qhia zaub mov nco. Ob txoj kab yuav txhua qhov tso saib ua ntej thiab tshuaj xyuas cov duab, thiab lub thib peb axis yuav tso saib keeb kwm ntawm pixels rau qhov saib ua ntej "xaiv" duab. Lub thawv hloov kho (cov ntawv) lub thawv yuav tso saib cov ntawv ntawm txoj kev xaiv cov duab, thiab daim teb hloov kho (lej) yuav tso saib pom thaj tsam ntawm lub ntsws.

Tam sim no hloov los ntawm kev tsim saib rau hauv kev saib pom hauv App Designer. Nkag mus rau hauv qhov chaws tus lej rau cov khoom los ntawm txhaj rau lub pob "Properties" liab nrog lub cim ntxiv los ntawm nws. Pib ua ntej cov khoom Kuv, qhov pib, thiab thaj tsam ToExtract raws li hauv cov cai hauv qab no. Tom ntej no, nyem rau lub pob nyob rau sab xis sab xis ntawm thaj chaw ua haujlwm (Tus Txheej Txheem Browser) thiab mus los ntawm Callbacks> Mus rau… callback. Ntxiv cov cai rau "ua haujlwm SelectImageButtonPushed (app, xwm txheej)." Txoj cai no tso cai rau koj xaiv cov duab los tshuaj xyuas los ntawm koj lub computer siv uigetfile. Tom qab xaiv ib daim duab, daim duab saib ua ntej yuav tshwm nyob rau hauv qab cov kab ntawv nrog los ntawm keeb kwm yav dhau. Tom qab ntawd, txoj cai-nyem rau lwm lub pob thiab rov ua cov txheej txheem qub los tsim kev hu xov tooj.

Ntxiv rau hauv cov cai hauv qab "ua haujlwm AnalyzeImageButtonPushed (app, xwm txheej)." Txoj cai no yuav ua tus lej pixel suav thiab nrhiav pom blob ntawm qhov saib ua ntej thaum tshawb xyuas cov duab khawm (qhov twg los xij uas koj tau nyem rau tus lej no). Tom qab teeb tsa cov nyees khawm, peb tam sim no yuav teeb tsa lub slider thiab cov ntawv qhia zaub mov nco-down. Txoj cai-nyem qhov slider, tsim kev hu rov qab thiab ntxiv rau cov lej hauv qab "ua haujlwm FilterThresholdSliderValueChanged (app, xwm txheej)" kom txog thaum kawg. Qhov no tso cai rau tus slider los kho qhov grey-siv qhov pib.

Tsim kom muaj kev hu rov qab rau cov ntawv qhia zaub mov nco, thiab ntxiv rau cov lej hauv qab "ua haujlwm AreastoExtractDropDownValueChanged (app, xwm txheej)" kom tso rau hauv cov ntawv qhia zaub mov hloov kho cov naj npawb ntawm blobs pom ntawm cov duab tsom xam. Tam sim no, nyem rau txhua qhov chaw hauv Component Browser thiab hloov lawv lub zog rau koj nyiam, xws li hloov cov npe ntawm cov koomhaum, tshem cov qag, thiab hloov pauv. Luag thiab tso cov khoom ntawm Component Browser hauv Tsim Saib kom ua haujlwm tau yooj yim thiab nkag siab yooj yim. Tam sim no koj muaj app hauv MATLAB uas tuaj yeem tshuaj xyuas cov duab ntawm lub ntsws rau thaj tsam pixel!

khoom (Nkag mus = ntiag tug) Kuv = ; % cov ntaub ntawv duab

pib = 257; %qhov pib rau binarizing siv zog grey

regionsToExtract = 2;

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muaj nuj nqi SelectImageButtonPushed (app, xwm txheej)

clc; Dir = 'C: / Users / danie / Downloads / images_004 / images'; %txheeb xyuas cov ntaub ntawv tsis raug "ua ntej"

[imageExt, path] = uigetfile ('*. png'); %lob qhov sib txawv ntawm lub npe duab

imageName = [Dir filesep imageExt]; %sib koom ua ke tsis sib xws thiab cov hlua sib txawv

app. I = imread (imageName); %nyeem cov duab

imshow (app. I, 'niam txiv', app. UIAxes); %tso saib daim duab

app. FilePathEditField. Value = txoj kev; %tso saib cov ntaub ntawv ntawm qhov twg thawj daim duab los ntawm

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muaj nuj nqi Txheeb XyuasImageButtonPushed (app, xwm txheej)

originalImage = app. I;

originalImage = wiener2 (app. I, [5 5]); %dot-tshem tawm lim

histogram (app. AxesHistogram, app. I, 256); %tso saib histogram ntawm daim duab

a_thresh = originalImage> = app.threshold; % teeb tsa qhov pib no

labelImage = bwlabel (a_thresh);

khoom siv = thaj tsam cov khoom siv (a_thresh, 'tag nrho');

sortedSolidity = txheeb ([props. Solidity], 'nqis');

SB = sortedSolidity (1);

yog SB == 1 % SB tsuas lees txais kev sib tw == 1 lim tawm cov pob txha

SE = strel ('xwmfab', 3);

morphologicalGradient = imsubtract (imdilate (labelImage, SE), imerode (labelImage, SE));

daim npog = imbinarize (morphologicalGradient, 0.03);

SE = strel ('xwmfab', 2);

mask = imclose (mask, SE);

mask = imfill (daim npog, 'qhov');

daim npog = bwareafilt (daim npog, app.regionsToExtract);

% tswj tus naj npawb ntawm thaj tsam qhia

notMask = ~ daim npog;

daim npog = daim npog | bwpropfilt (notMask, 'Area', [-Inf, 5000 - eps (5000)]));

BW2 = imfill (labelImage, 'qhov');

new_image = BW2;

new_image (~ daim npog) = 0;

B = bwboundaries (tshiab_image); % tsuas tuaj yeem lees txais 2 qhov ntev imshow (new_image, 'niam txiv', app. UIAxes2);

tuav (app. UIAxes2, 'rau');

visboundaries (B);

teeb (gca, 'YDir', 'thim rov qab');

lungArea = bwarea (tshiab_image);

app. PixelAreaEditField. Value = lungArea;

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muaj nuj nqi FilterThresholdSliderValueChanged (app, xwm txheej)

app.threshold = app. FilterThresholdSlider. Value;

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muaj nuj nqi AreastoExtractDropDownValueChanged (app, xwm txheej) stringNumber = app. AreastoExtractDropDown. Value;

app.regionsToExtract = str2double (stringNumber);

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