diff --git a/AugmentedInSilico/GenSilicoAug/BubbleGT/BubbleGT10_Silico1.mat b/AugmentedInSilico/GenSilicoAug/BubbleGT/BubbleGT10_Silico1.mat
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diff --git a/AugmentedInSilico/GenSilicoAug/BubbleGT/BubbleGT2_Silico4.mat b/AugmentedInSilico/GenSilicoAug/BubbleGT/BubbleGT2_Silico4.mat
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diff --git a/AugmentedInSilico/GenSilicoAug/BubbleGT/BubbleGT2_Silico5.mat b/AugmentedInSilico/GenSilicoAug/BubbleGT/BubbleGT2_Silico5.mat
new file mode 100644
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diff --git a/AugmentedInSilico/GenSilicoAug/GenGT.m b/AugmentedInSilico/GenSilicoAug/GenGT.m
new file mode 100644
index 0000000000000000000000000000000000000000..97ac26f01172789d3cbf2874b9c03ecc64281e3b
--- /dev/null
+++ b/AugmentedInSilico/GenSilicoAug/GenGT.m
@@ -0,0 +1,18 @@
+
+SR=10;
+
+
+for hhh = 1:5
+BubbleGT=zeros(84*SR+1,143*SR+1,1000);
+
+load(strcat('MatTracks/MatTrackingSilicoAug',int2str(hhh),'.mat'))
+
+
+for kk = 1:length(MatTracking)
+ BubbleGT(max(1, round( MatTracking(kk,2)*SR)),max(1, round( MatTracking(kk,3)*SR)),MatTracking(kk,4))=BubbleGT(max(1, round( MatTracking(kk,2)*SR)),max(1, round( MatTracking(kk,3)*SR)),MatTracking(kk,4))+1;%MatTracking(kk,1)
+end
+
+
+BubbleGT= single(BubbleGT);
+ save(strcat('BubbleGT/BubbleGT',int2str(SR),'_Silico',int2str(hhh)), 'BubbleGT','-v7.3'); BubbleGT=[];
+end
diff --git a/AugmentedInSilico/GenSilicoAug/GenSilico.m b/AugmentedInSilico/GenSilicoAug/GenSilico.m
new file mode 100644
index 0000000000000000000000000000000000000000..071c95ad0007b8e168478f92b6f20aecab30c67e
--- /dev/null
+++ b/AugmentedInSilico/GenSilicoAug/GenSilico.m
@@ -0,0 +1,40 @@
+clear
+ IQ = load('TissueCrop.mat','IQ').IQ;
+
+
+ IQs = repmat(IQ,[1 1 1000]);
+ IQs = real(IQs);
+ BaseAmp = max(abs(IQs(:)));
+ IQs=IQs/BaseAmp;
+ MeanPowClutter = mean(abs(IQs(:)).^2);
+ TargetPowFlow = MeanPowClutter/(10^2);
+
+ijk = {'0','10','20','40'};
+
+load('SimusPSF.mat', 'RFb');
+for hhh = 1:5
+
+ GTs = load(strcat(pwd,'/BubbleGT/BubbleGT10_Silico',int2str(hhh),'.mat'),'BubbleGT').BubbleGT;
+ GTs = GTs(1:end-1,1:end-1,:);
+ GTs = imfilter(GTs, RFb,'conv','circular');
+
+ GTs = imresize(GTs,[84 143],'bicubic');
+
+ GTs= GTs/max(abs(GTs(:)));
+ temp = abs(GTs);
+ MeanPowFlow = mean(temp(temp>0).^2);
+ GTs_T = GTs*sqrt(TargetPowFlow/MeanPowFlow);
+
+
+ for kkk = 1:4
+ SNR = ijk{kkk};
+
+ Noise = RAWGN_SNR(GTs_T, str2double(SNR));
+ SilicoAug = GTs_T + IQs + Noise;
+ SilicoAug = BaseAmp*SilicoAug/max(abs(SilicoAug(:)));
+ save(fullfile(fileparts(pwd), strcat('SilicoData_',SNR,'dB/SilicoAug',int2str(hhh),'.mat')), 'SilicoAug');
+
+
+ end
+
+end
\ No newline at end of file
diff --git a/AugmentedInSilico/GenSilicoAug/MatTrackSilicoAugGen.m b/AugmentedInSilico/GenSilicoAug/MatTrackSilicoAugGen.m
new file mode 100644
index 0000000000000000000000000000000000000000..8a8ce61a338c5c25bd4b805931f465c7e2d30b83
--- /dev/null
+++ b/AugmentedInSilico/GenSilicoAug/MatTrackSilicoAugGen.m
@@ -0,0 +1,29 @@
+clear
+load('PALA_InSilicoFlow_v3_pos_MediaPos.mat')
+
+
+for hhh = 1:5
+ MatTracking = [];
+
+for NumFrame = [1000*(hhh-1)+1:1000*hhh 1000*(hhh+5-1)+1:1000*(hhh+5) 1000*(hhh+10-1)+1:1000*(hhh+10) 1000*(hhh+15-1)+1:1000*(hhh+15)]
+temp=MediaPos{NumFrame};
+temp(:,1) = temp(:,1) + 72 +1;
+temp(:,3) = temp(:,3) - 16 +1;
+
+ for Numbulles = 1:size(temp,1)
+
+ if (round(temp(Numbulles,3))> 0 && temp(Numbulles,3)< 84.05 && round(temp(Numbulles,1))> 0 && temp(Numbulles,1)< 143.05)
+ Yvalue = temp(Numbulles,2);
+ MatTracking = cat(1,MatTracking, [exp(-Yvalue^2/2.3) temp(Numbulles,3) temp(Numbulles,1) mod(NumFrame,1000)]);
+
+ end
+ end
+
+end
+
+MatTracking(MatTracking(:, end) == 0, end) = 1000;
+
+MatTracking = sortrows(MatTracking,4);
+
+save(['MatTrackingSilicoAug',int2str(hhh),'.mat'],'MatTracking')
+end
\ No newline at end of file
diff --git a/AugmentedInSilico/GenSilicoAug/MatTracks/MatTrackingSilicoAug1.mat b/AugmentedInSilico/GenSilicoAug/MatTracks/MatTrackingSilicoAug1.mat
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index 0000000000000000000000000000000000000000..765a14b3d7aa5f1031566f683537b648b88360ad
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diff --git a/AugmentedInSilico/GenSilicoAug/MatTracks/MatTrackingSilicoAug2.mat b/AugmentedInSilico/GenSilicoAug/MatTracks/MatTrackingSilicoAug2.mat
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index 0000000000000000000000000000000000000000..0faa344a821e4790f8b12fe958d5fe732490a14c
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diff --git a/AugmentedInSilico/GenSilicoAug/MatTracks/MatTrackingSilicoAug3.mat b/AugmentedInSilico/GenSilicoAug/MatTracks/MatTrackingSilicoAug3.mat
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index 0000000000000000000000000000000000000000..97a0de132099ed9fb618ef8d25bbb226f1d56316
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diff --git a/AugmentedInSilico/GenSilicoAug/MatTracks/MatTrackingSilicoAug4.mat b/AugmentedInSilico/GenSilicoAug/MatTracks/MatTrackingSilicoAug4.mat
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index 0000000000000000000000000000000000000000..f78177db4b94a4fd55fb8c321a5128db1805e739
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diff --git a/AugmentedInSilico/GenSilicoAug/MatTracks/MatTrackingSilicoAug5.mat b/AugmentedInSilico/GenSilicoAug/MatTracks/MatTrackingSilicoAug5.mat
new file mode 100644
index 0000000000000000000000000000000000000000..5bf22fe56361ee266303a4e5e163eb4e5e033f73
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diff --git a/AugmentedInSilico/GenSilicoAug/PALA_InSilicoFlow_v3_pos_MediaPos.mat b/AugmentedInSilico/GenSilicoAug/PALA_InSilicoFlow_v3_pos_MediaPos.mat
new file mode 100644
index 0000000000000000000000000000000000000000..5b4dddb9f5f8ec0c32e56387c26d1a42cedbc8ef
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diff --git a/AugmentedInSilico/GenSilicoAug/RAWGN_SNR.m b/AugmentedInSilico/GenSilicoAug/RAWGN_SNR.m
new file mode 100644
index 0000000000000000000000000000000000000000..c51680cbc42950aa2e14a3ffed532369d8895050
--- /dev/null
+++ b/AugmentedInSilico/GenSilicoAug/RAWGN_SNR.m
@@ -0,0 +1,13 @@
+function noise = RAWGN_SNR(myimage, SNRdB)
+
+output_image = myimage;
+SNR=(10^(SNRdB/10));
+
+
+ps_in = mean(abs(output_image(:)).^2);
+
+pb_norm = ps_in/SNR;
+noise=sqrt(pb_norm)* randn(size(output_image));
+end
+
+
diff --git a/AugmentedInSilico/GenSilicoAug/SimusPSF.mat b/AugmentedInSilico/GenSilicoAug/SimusPSF.mat
new file mode 100644
index 0000000000000000000000000000000000000000..643e843354dcdd5ee0f8a92c32ca24e67b412850
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diff --git a/AugmentedInSilico/GenSilicoAug/SimusPSFGen/PSFgen.m b/AugmentedInSilico/GenSilicoAug/SimusPSFGen/PSFgen.m
new file mode 100644
index 0000000000000000000000000000000000000000..d888f7f64c37c0a075a4f1bb43796f29eb9ec8b5
--- /dev/null
+++ b/AugmentedInSilico/GenSilicoAug/SimusPSFGen/PSFgen.m
@@ -0,0 +1,59 @@
+% Adapted from the code written by Adrian Basarab
+
+% clear;
+% clc;
+
+% MUST (SIMUS) path
+addpath(genpath('...\Documents\MATLAB\MUST'));
+
+%-- Ultrasound probe
+probe = 192;
+% if isequal(probe,192)
+%
+% elseif isequal(probe,128)
+% probe = 'L11-5v';
+% end
+probe = 'L22-14V';
+
+%-- Parameters of the ultrasound probe
+param = getparam(probe);
+L = param.pitch*(param.Nelements-1); % width of the full aperture
+lambda = 1540/param.fc;
+
+%-- Sub-apertures
+% number of elements used to generate one focused beam
+if param.Nelements==192, Ne = 32; else, Ne = 24; end
+param.Nelements = 192;
+
+%-- One scatterer
+xs = [0 0];
+zs = [L/2 L];
+RC = [1 0];
+
+%-- Transmit delays for a focused trasnmit
+xf = 0; zf = L/2;
+txdel = txdelay(xf,zf,param);
+
+%-- Simulations of the RF signals with SIMUS
+param.fs = 4*param.fc; % sampling frequency in Hz
+option = [];
+RF = simus(xs,zs,RC,txdel,param,option);
+
+%-- DAS beamforming
+step = lambda/20;
+[x,z] = meshgrid(-4*param.pitch:step:4*param.pitch,(-2*param.pitch:param.pitch/20:2*param.pitch)+L/2); %param.pitch/2
+param.fnumber = [];
+RFb = das(RF,x,z,txdel,param,'lanczos3');
+
+
+%-- Display the RF PSF
+figure(101)
+imagesc(x(1,:)*1e3,(z(:,1)-L/2)*1e3,RFb)
+colormap([1-hot; hot])
+axis equal ij tight
+xlabel('[mm]'),ylabel('[mm]')
+
+%% Envelope
+RFb = abs(hilbert(RFb));
+figure
+surf(RFb)
diff --git a/AugmentedInSilico/GenSilicoAug/SimusPSFGen/getparam.m b/AugmentedInSilico/GenSilicoAug/SimusPSFGen/getparam.m
new file mode 100644
index 0000000000000000000000000000000000000000..646a1ac927ba46969d4cc258c32079090751bc2c
--- /dev/null
+++ b/AugmentedInSilico/GenSilicoAug/SimusPSFGen/getparam.m
@@ -0,0 +1,205 @@
+function param = getparam(probe)
+
+%GETPARAM Get parameters of a uniform linear or convex array
+% PARAM = GETPARAM opens a dialog box which allows you to select a
+% transducer whose parameters are returned in PARAM.
+%
+% PARAM = GETPARAM(PROBE), where PROBE is a string, returns the prameters
+% of the transducer given by PROBE.
+%
+% The structure PARAM is used in several functions of MUST (Matlab
+% UltraSound Toolbox). The structure returned by GETPARAM contains only
+% the fields that describe a transducer. Other fields may be required in
+% some MUST functions.
+%
+% PROBE can be one of the following:
+% ---------------------------------
+% 1) 'L11-5v' (128-element, 7.6-MHz linear array)
+% 2) 'L12-3v' (192-element, 7.5-MHz linear array)
+% 3) 'C5-2v' (128-element, 3.6-MHz convex array)
+% 4) 'P4-2v' (64-element, 2.7-MHz phased array)
+%
+% These are the <a
+% href="matlab:web('https://verasonics.com/verasonics-transducers/')">Verasonics' transducers</a>.
+% Feel free to complete this list for your own use.
+%
+% PARAM is a structure that contains the following fields:
+% --------------------------------------------------------
+% 1) PARAM.Nelements: number of elements in the transducer array
+% 2) PARAM.fc: center frequency (in Hz)
+% 3) PARAM.pitch: element pitch (in m)
+% 4) PARAM.width: element width (in m)
+% 5) PARAM.kerf: kerf width (in m)
+% 6) PARAM.bandwidth: 6-dB fractional bandwidth (in %)
+% 7) PARAM.radius: radius of curvature (in m, Inf for a linear array)
+% 8) PARAM.focus: elevation focus (in m)
+% 9) PARAM.height: element height (in m)
+%
+%
+% Example:
+% -------
+% %-- Generate a focused pressure field with a phased-array transducer
+% % Phased-array @ 2.7 MHz:
+% param = getparam('P4-2v');
+% % Focus position:
+% x0 = 2e-2; z0 = 5e-2;
+% % TX time delays:
+% dels = txdelay(x0,z0,param);
+% % Grid:
+% x = linspace(-4e-2,4e-2,200);
+% z = linspace(param.pitch,10e-2,200);
+% [x,z] = meshgrid(x,z);
+% y = zeros(size(x));
+% % RMS pressure field:
+% P = pfield(x,y,z,dels,param);
+% imagesc(x(1,:)*1e2,z(:,1)*1e2,20*log10(P/max(P(:))))
+% hold on, plot(x0*1e2,z0*1e2,'k*'), hold off
+% colormap hot, axis equal tight
+% caxis([-20 0])
+% c = colorbar;
+% c.YTickLabel{end} = '0 dB';
+% xlabel('[cm]')
+%
+%
+% This function is part of <a
+% href="matlab:web('https://www.biomecardio.com/MUST')">MUST</a> (Matlab UltraSound Toolbox).
+% MUST (c) 2020 Damien Garcia, LGPL-3.0-or-later
+%
+% See also TXDELAY, PFIELD, SIMUS, GETPULSE.
+%
+% -- Damien Garcia -- 2015/03, last update: 2020/07
+% website: <a
+% href="matlab:web('https://www.biomecardio.com')">www.BiomeCardio.com</a>
+
+if nargin==0
+ ProbeList = {'L11-5v','L12-3v','C5-2v','P4-2v',...
+ 'LA530','L14-5/38','L14-5W/60','L9-4/38','PA4-2/20','P6-3'};
+ ProbeList = sort(ProbeList);
+ selection = listdlg('ListString',ProbeList,...
+ 'PromptString','Select a probe:',...
+ 'SelectionMode','single');
+ try
+ probe = ProbeList{selection};
+ catch
+ param = struct([]);
+ return
+ end
+end
+
+
+switch upper(probe)
+ case 'L11-5V'
+ % --- L11-5v (Verasonics) ---
+ param.fc = 7.6e6; % Transducer center frequency [Hz]
+ param.kerf = 30e-6; % Kerf [m]
+ param.width = 270e-6; % Width [m]
+ param.pitch = 300e-6; % Pitch [m]
+ param.Nelements = 128;
+ param.bandwidth = 77; % Fractional bandwidth [%]
+ param.radius = Inf;
+ param.height = 5e-3; % Elevation height [m]
+ param.focus = 18e-3; % Elevation focus [m]
+ case 'L22-14V'
+ % --- L22-14v (Verasonics) ---
+ param.fc = 15.625e6; % Transducer center frequency [Hz] %% ok
+ param.kerf = 20e-6; % Kerf [m]
+ param.width = 80e-6; % Width [m] %% ok
+ param.pitch = 100e-6; % Pitch [m] %% ok
+ param.Nelements = 128; %% ok
+ param.bandwidth = 87; % Fractional bandwidth [%] %% 14,22
+ param.radius = Inf; %% ok
+ param.height = 6e-3; % Elevation height [m]
+ param.focus = 8e-3; % Elevation focus [m] %% ok
+ case 'L12-3V'
+ % --- L12-3v (Verasonics) ---
+ param.fc = 7.5e6; % Transducer center frequency [Hz]
+ param.kerf = 30e-6; % Kerf [m]
+ param.width = 170e-6; % Width [m]
+ param.pitch = 200e-6; % Pitch [m]
+ param.Nelements = 192;
+ param.bandwidth = 93; % Fractional bandwidth [%]
+ param.radius = Inf;
+ param.height = 5e-3; % Elevation height [m]
+ param.focus = 20e-3; % Elevation focus [m]
+ case 'C5-2V'
+ % --- C5-2v (Verasonics) ---
+ param.fc = 3.6e6; % Transducer center frequency [Hz]
+ param.kerf = 48e-6; % Kerf [m]
+ param.width = 460e-6; % Width [m]
+ param.pitch = 508e-6; % Pitch [m]
+ param.Nelements = 128;
+ param.bandwidth = 80; % Fractional bandwidth [%]
+ param.radius = 49.6e-3; % Array radius [m]
+ param.height = 13.5e-3; % Elevation height [m]
+ param.focus = 60e-3; % Elevation focus [m]
+ case 'P4-2V'
+ % --- P4-2v (Verasonics) ---
+ param.fc = 2.7e6; % Transducer center frequency [Hz]
+ param.kerf = 50e-6; % Kerf [m]
+ param.width = 250e-6; % Width [m]
+ param.pitch = 300e-6; % Pitch [m]
+ param.Nelements = 64;
+ param.bandwidth = 74; % Fractional bandwidth [%]
+ param.radius = Inf;
+ param.height = 14e-3; % Elevation height [m]
+ param.focus = 60e-3; % Elevation focus [m]
+
+
+ %--- From the OLD version of GETPARAM: ---%
+
+ case 'PA4-2/20'
+ % --- PA4-2/20 ---
+ param.fc = 2.5e6; % Transducer center frequency [Hz]
+ param.kerf = 50e-6; % Kerf [m]
+ param.pitch = 300e-6; % Pitch [m]
+ % height = 14e-6; % Height of element [m]
+ param.Nelements = 64;
+ param.bandwidth = 60; % Fractional bandwidth [%]
+ case 'L9-4/38'
+ % --- L9-4/38 ---
+ param.fc = 5e6; % Transducer center frequency [Hz]
+ param.kerf = 35e-6; % Kerf [m]
+ param.pitch = 304.8e-6; % Pitch [m]
+ % 6/1000; % Height of element [m]
+ param.Nelements = 128;
+ param.bandwidth = 65; % Fractional bandwidth [%]
+ case 'LA530'
+ % --- LA530 ---
+ param.fc = 3e6; % Transducer center frequency [Hz]
+ width = 0.215/1000; %0.2698/1000; % Width of element [m]
+ param.kerf = 0.030/1000; %0.035/1000; % Kerf [m]
+ param.pitch = width + param.kerf;
+ % element_height = 6/1000; % Height of element [m]
+ param.Nelements = 192;
+ case 'L14-5/38'
+ % --- L14-5/38 ---
+ param.fc = 7.2e6; % Transducer center frequency [Hz]
+ param.kerf = 25e-6; % Kerf [m]
+ param.pitch = 304.8e-6; % Pitch [m]
+ % height = 4e-3; % Height of element [m]
+ param.Nelements = 128;
+ param.bandwidth = 70; % Fractional bandwidth [%]
+ case 'L14-5W/60'
+ % --- L14-5W/60 ---
+ param.fc = 7.5e6; % Transducer center frequency [Hz]
+ param.kerf = 25e-6; % Kerf [m]
+ param.pitch = 472e-6; % Pitch [m]
+ % height = 4e-3; % Height of element [m]
+ param.Nelements = 128;
+ param.bandwidth = 65; % Fractional bandwidth [%]
+ case 'P6-3'
+ % --- P6-3 ---
+ param.fc = 4.5e6; % Transducer center frequency [Hz]
+ param.kerf = 25e-6; % Kerf [m]
+ param.pitch = 218e-6; % Pitch [m]
+ param.Nelements = 64;
+ param.bandwidth = 2/3*100; % Fractional bandwidth [%]
+
+
+
+ otherwise
+ error(['The probe ' probe ' is unknown.',...
+ ' You may complete this function for your own use'])
+end
+
+
diff --git a/AugmentedInSilico/GenSilicoAug/TissueCrop.mat b/AugmentedInSilico/GenSilicoAug/TissueCrop.mat
new file mode 100644
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