diff --git a/readme.md b/readme.md
index 73d3cc913d672c5ee9ac0ebe4913748527f00867..a1364b0961aba2359c369743a3adcc29f5f887e1 100644
--- a/readme.md
+++ b/readme.md
@@ -44,7 +44,7 @@ path(path, 'PATH\hydra-image-processor\src\MATLAB');
 # USE
 
 To recreate Figure 6:
-1. Run phantomVelocitySSF\goFigure.m
+1. Run phantomVelocitySSF\genPhantomVelocityFigure.m
 
 ## Phantom Velocity SSF Dataset Generation
 To create a new synethetic dataset:
@@ -54,7 +54,7 @@ To create a new synethetic dataset:
     - phantomVelocity_mu: the different mean velocity values per class i.e., the number of means determines the number of classes.
     - phantomVelocity_sigma: the standard deviation for velocity per class.
     - numOutput: how many phantom images to generate per class.
-2. Run phantomVelocitySSF\goFigure.m, specifying the saved .mat file as the input.
+2. Run phantomVelocitySSF\genPhantomVelocityFigure.m, specifying the saved .mat file as the input.
 
 ## Notes
 1. The NCD code uses the [FLIF](https://flif.info/) compression library. The thunker file for the FLIF library was generated on Ubuntu 22.04 and **may not work** on other Unix platforms.  
@@ -62,3 +62,5 @@ This has not been tested.
 The Windows version works on both Windows 10 and Windows 11.
 2. The default settings for phantomVelocitySSF\goSyntheticDataset will create a dataset of 150 phantom velocity SSF images.  
 This can be CPU intensive. For testing purposes it is recommended to lower the number of generated images (numOutput) to 5-10. 
+
+## Phantom SSF
diff --git a/src/MATLAB/phantomSSF/genPhantomFigure.asv b/src/MATLAB/phantomSSF/genPhantomFigure.asv
new file mode 100644
index 0000000000000000000000000000000000000000..8f6feb3eae1946e926510d4429d34d4f2679d4f4
--- /dev/null
+++ b/src/MATLAB/phantomSSF/genPhantomFigure.asv
@@ -0,0 +1,72 @@
+
+cnRatios = zeros(9,100);
+ccnRatios = zeros(9,100);
+ssfVals = zeros(9,100);
+
+% i = 9;
+
+for i = 1:10
+    for j = 1:100
+        % [cnRatio,ssfVal] = ssfPhantom(i/10);
+        % [cnRatio,ccnRatio,ssfVal] = ssfPhantom((i-1)/10);
+        [cnRatio,ccnRatio,ssfVal] = ssfPhantom
+
+        cnRatios(i,j) = cnRatio;
+        ssfVals(i,j) = ssfVal;
+        ccnRatios(i,j) = ccnRatio;
+    end
+end
+
+4;
+
+[cnRefVal,ssfRefVal] = ssfPhantom(0);
+
+mc = mean(cnRatios,2);
+sc = std(cnRatios,0,2);
+ms = mean(ssfVals,2);
+ss = std(ssfVals,0,2);
+
+mccn = mean(ccnRatios,2);
+sccn = std(ccnRatios,0,2);
+
+msNorm = mean(ssfVals,2)./ssfRefVal;
+ssNorm = std(ssfVals./ssfRefVal,0,2);
+
+% figure('WindowState','maximized');
+figure;
+
+plot([1:-.1:.1],'color','y','LineWidth',4,'linestyle','-'); hold on;
+errorbar(mc,sc/(2*sqrt(size(ssfVals,2))),'color','r')
+errorbar(mccn,sccn/(2*sqrt(size(ssfVals,2))),'color',[0.4660 0.6740 0.1880])
+errorbar(ms,ss/(2*sqrt(size(ssfVals,2))),'color','m')
+% errorbar(msNorm,ssNorm/(2*sqrt(size(ssfVals,2))),'-ro','color','k','markersize',8,'markerfacecolor','r');
+errorbar(msNorm,ssNorm/(2*sqrt(size(ssfVals,2))),'color','k');
+
+for i = 0:9
+    l = [num2str(i*10) '%'];
+    xlab{i+1} = l;
+end
+    
+xticklabels(xlab)
+% xlabel('Percentage of Noise Applied to Reference Image');
+xlabel('Percentage of signal added to nucleus and cytoplasm');
+ylabel('Cell signal activation')
+% set(gca, 'YScale', 'log')
+
+% legend('GT','Nuclear/Cyto Ratio','LoG','SSF')
+% legend('GT','CN_{ratio}','LoG','SSF','\frac{C}{C+N}')
+legend('GT','$\frac{C}{N}$','$\frac{C}{C+N}$','LoG','SSF','Interpreter','latex')
+set(gcf,'color','white')
+ylim([0 5])
+
+f = getframe(gcf);
+
+cap = frame2im(f);
+outName = 'phantomLinear.tif';
+outRoot = './';
+
+outFile = fullfile(outRoot,outName);
+imwrite(cap,outFile);
+
+
+4;
\ No newline at end of file
diff --git a/src/MATLAB/ssf_vs_cn/goFigure3C.m b/src/MATLAB/phantomSSF/genPhantomFigure.m
similarity index 92%
rename from src/MATLAB/ssf_vs_cn/goFigure3C.m
rename to src/MATLAB/phantomSSF/genPhantomFigure.m
index e44eb3b545e2e00da09716f154096fbbbd6434ea..ea0201e01cf5455301bfa89e7d1ac1f643cdd708 100644
--- a/src/MATLAB/ssf_vs_cn/goFigure3C.m
+++ b/src/MATLAB/phantomSSF/genPhantomFigure.m
@@ -7,10 +7,9 @@ ssfVals = zeros(9,100);
 
 for i = 1:10
     for j = 1:100
-        
-%         [cnRatio,ssfVal] = ssfPhantom(i/10);
-        [cnRatio,ccnRatio, ssfVal] = ssfPhantom((i-1)/10);
-        
+        % [cnRatio,ssfVal] = ssfPhantom(i/10);
+        [cnRatio,ccnRatio,ssfVal] = ssfPhantom((i-1)/10);
+
         cnRatios(i,j) = cnRatio;
         ssfVals(i,j) = ssfVal;
         ccnRatios(i,j) = ccnRatio;
diff --git a/src/MATLAB/ssf_vs_cn/goPhantomImage.m b/src/MATLAB/phantomSSF/goPhantomImage.m
similarity index 100%
rename from src/MATLAB/ssf_vs_cn/goPhantomImage.m
rename to src/MATLAB/phantomSSF/goPhantomImage.m
diff --git a/src/MATLAB/ssf_vs_cn/goSSF_CN.m b/src/MATLAB/phantomSSF/goSSF_CN.m
similarity index 100%
rename from src/MATLAB/ssf_vs_cn/goSSF_CN.m
rename to src/MATLAB/phantomSSF/goSSF_CN.m
diff --git a/src/MATLAB/ssf_vs_cn/ssfPhantom.m b/src/MATLAB/phantomSSF/ssfPhantom.m
similarity index 94%
rename from src/MATLAB/ssf_vs_cn/ssfPhantom.m
rename to src/MATLAB/phantomSSF/ssfPhantom.m
index fbddbe8c8d7f0f1dc001393b30a8779167a4ad67..f41dac56df8aee0cdfc93a84d1d7a95951c55146 100644
--- a/src/MATLAB/ssf_vs_cn/ssfPhantom.m
+++ b/src/MATLAB/phantomSSF/ssfPhantom.m
@@ -1,4 +1,4 @@
-function [cnRatio,ccnRatio, ssfValue] = ssfPhantom(density)
+function [cnRatio,ccnRatio,ssfValue] = ssfPhantom(density)
 
 % set width/length of the image
 wl = 200;
diff --git a/src/MATLAB/phantomKymograph/createPhantom.m b/src/MATLAB/phantomVelocitySSF/createPhantom.m
similarity index 100%
rename from src/MATLAB/phantomKymograph/createPhantom.m
rename to src/MATLAB/phantomVelocitySSF/createPhantom.m
diff --git a/src/MATLAB/phantomKymograph/createSyntheticDataset.m b/src/MATLAB/phantomVelocitySSF/createSyntheticDataset.m
similarity index 100%
rename from src/MATLAB/phantomKymograph/createSyntheticDataset.m
rename to src/MATLAB/phantomVelocitySSF/createSyntheticDataset.m
diff --git a/src/MATLAB/phantomKymograph/drawSyntheticSSF.m b/src/MATLAB/phantomVelocitySSF/drawSyntheticSSF.m
similarity index 100%
rename from src/MATLAB/phantomKymograph/drawSyntheticSSF.m
rename to src/MATLAB/phantomVelocitySSF/drawSyntheticSSF.m
diff --git a/src/MATLAB/phantomKymograph/goFigure.m b/src/MATLAB/phantomVelocitySSF/genPhantomVelocityFigure.m
similarity index 100%
rename from src/MATLAB/phantomKymograph/goFigure.m
rename to src/MATLAB/phantomVelocitySSF/genPhantomVelocityFigure.m
diff --git a/src/MATLAB/phantomKymograph/getPhantomClipLimits.m b/src/MATLAB/phantomVelocitySSF/getPhantomClipLimits.m
similarity index 100%
rename from src/MATLAB/phantomKymograph/getPhantomClipLimits.m
rename to src/MATLAB/phantomVelocitySSF/getPhantomClipLimits.m
diff --git a/src/MATLAB/phantomKymograph/goSyntheticDataset.m b/src/MATLAB/phantomVelocitySSF/goSyntheticDataset.m
similarity index 100%
rename from src/MATLAB/phantomKymograph/goSyntheticDataset.m
rename to src/MATLAB/phantomVelocitySSF/goSyntheticDataset.m
diff --git a/src/MATLAB/phantomKymograph/goSyntheticSSF.m b/src/MATLAB/phantomVelocitySSF/goSyntheticSSF.m
similarity index 100%
rename from src/MATLAB/phantomKymograph/goSyntheticSSF.m
rename to src/MATLAB/phantomVelocitySSF/goSyntheticSSF.m
diff --git a/src/MATLAB/phantomKymograph/sampleDataset_01.mat b/src/MATLAB/phantomVelocitySSF/sampleDataset_01.mat
similarity index 100%
rename from src/MATLAB/phantomKymograph/sampleDataset_01.mat
rename to src/MATLAB/phantomVelocitySSF/sampleDataset_01.mat
diff --git a/src/MATLAB/ssf_vs_cn/phantomLinear.tif b/src/MATLAB/ssf_vs_cn/phantomLinear.tif
deleted file mode 100644
index e53eae496b03a35d5f5daf4f62c6e3505acb5285..0000000000000000000000000000000000000000
Binary files a/src/MATLAB/ssf_vs_cn/phantomLinear.tif and /dev/null differ