Replace inPhase_Segmentation_v11.m

inPhase_Segmentation_v11.m

 %% inPhase segemntation routine
 % It assumes pairs of BF images and fluorescent maximum projections in .tif format
 % These pairs should have the same name with "BF" and "Max" as labels.
-% these pairs are supposed to have the used temperature in the name of the file (_xxC_)
+% These pairs are supposed to have the used temperature in the name of the file (_xxC_)
 % Example:
 % BF_proteinName_20C
 % Max_proteinName_20C
@@ -13,7 +13,7 @@ filesTiff = dir([pathi '/**/*.tif']);
 folderExp = unique({filesTiff.folder});
 
 % Save images of segmentation for all individual emulsion droplets
-saveImage = true;
+saveImage = false;
 
 % Experimental setup related constants
 pixelSize = 0.1625; 
@@ -300,7 +300,18 @@ for k = 1 : length(folderExp)
             currImageCropBF = imgaussfilt(currImageCropBF, 3);
             currImageCropBF2 = imgradient(currImageCropBF);
             currImageCropBF2(~emulsionMask) = mean(currImageCropBF2(emulsionMask));
-            [centerBF, radiusBF, metricBF] = imfindcircles(imadjust(currImageCropBF2), [10, round(size(currImageCropBF2, 1)/5)], 'Sensitivity', 0.6, 'ObjectPolarity', 'dark');
+            [centerBF, radiusBF, ~] = imfindcircles(imadjust(currImageCropBF2), [10, round(size(currImageCropBF2, 1)/5)], 'Sensitivity', 0.6, 'ObjectPolarity', 'dark');
+            % remove misdetection of bright spots
+            if ~isempty(centerBF)
+                currImageCropBF_Mask = createCirclesMask(size(currImageCropBF), centerBF, radiusBF);
+                currImageCropBF_Mask = regionprops(currImageCropBF_Mask, currImageCropBF, 'MeanIntensity', 'Centroid');
+                currImageCropBF_Int = vertcat(currImageCropBF_Mask.MeanIntensity);
+                currImageCropBF_Centroid = vertcat(currImageCropBF_Mask.Centroid);
+                currIndx = currImageCropBF_Int <= mean(currImageCropBF(emulsionMask));
+                currIndx = sum(abs(centerBF - currImageCropBF_Centroid(currIndx, :)),2) <= 2;
+                centerBF = centerBF(currIndx, :);
+                radiusBF = radiusBF(currIndx);
+            end
             if saveImage
                 hf1 = figure('visible', 'off');
                 imshow(currImageCropBF)
@@ -370,5 +381,4 @@ for k = 1 : length(folderExp)
     % save Output data as .mat
     save([currFolderExp{1}, filesep, 'ResultsNew.mat'], 'Results')
     
-end
-
+end
\ No newline at end of file