Improvements

daniel/label_by_size.m

@@ -0,0 +1,9 @@
+stats=regionprops(labelled_cyto,'area');
+area = cat(1, stats.Area);
+labelled_by_size = zeros(size(labelled_cyto));
+for cell_id=1:max(labelled_cyto(:))
+  labelled_by_size(labelled_cyto==cell_id)=area(cell_id);
+end
+COLOR_LIMIT = prctile(ResultsTable.CellSize,98);
+labelled_by_size(labelled_by_size>COLOR_LIMIT)=COLOR_LIMIT; % make colors more beautiful by putting an upper limit
+figure; imshow3Dfull(labelled_by_size,[])

daniel/overview_images.m

@@ -77,13 +77,13 @@
   zmin = ceil(boundingbox(3));
   zmax = ceil(boundingbox(3)) + ceil(boundingbox(6)) - 1;
   cyto=cyto(xmin:xmax,ymin:ymax,zmin:zmax); % crop
-  % figure('name','cyto_cropped','NumberTitle', 'off'); imshow3D(cyto,[]);
+  % figure('name','cyto_cropped','NumberTitle', 'off'); imshow3Dfull(cyto,[]);
   %% CROP NUC
   nuc=nuc(xmin:xmax,ymin:ymax,zmin:zmax); % crop;
-  % figure('name','nuc_cropped','NumberTitle', 'off'); imshow3D(nuc,[]);
+  % figure('name','nuc_cropped','NumberTitle', 'off'); imshow3Dfull(nuc,[]);
   %% CROP INSULIN
   insulin=insulin(xmin:xmax,ymin:ymax,zmin:zmax); % crop
-  % figure('name','insulin_cropped','NumberTitle', 'off'); imshow3D(insulin,[]);
+  % figure('name','insulin_cropped','NumberTitle', 'off'); imshow3Dfull(insulin,[]);
 
   nuc1 = nuc(:,:,2); % first
   nuc2 = nuc(:,:,floor(size(nuc,3)/2)); % middle

daniel/single-cell-slices-visualization.m

@@ -0,0 +1,160 @@
+% THIS WAS TAKEN FROM OLD CODE
+
+set(0,'DefaultFigureWindowStyle','docked')
+addpath 'Matlab function library'
+f = funcs;
+inpath = 'Islet_whole_mount_cy2pdx_cy3E-cad_cy5SE_DAPI_141116\Tiff_7_Dapi_cy3_cy2';
+
+data.sections = [];
+
+%% Load 3d image from folder.
+% tiff images with 3 channels: e-cadherin, protein marker and pdx1
+disp('Loading image..')
+zpic_DAPI = f.im3dread(inpath, '*.tif', 3); %Blue channel: DAPI
+zpic_ECad = f.im3dread(inpath, '*.tif', 1); %Red channel: e-cadherin
+
+% figure('name','nuc','NumberTitle', 'off');imshow3Dfull(zpic_DAPI,[])
+
+
+% Remove background, create bw.
+im_c = imclose(zpic_DAPI, f.strelball(1));
+% figure('name','im_c','NumberTitle', 'off');imshow3D(im_c,[])
+im_o = imopen(im_c, strel('disk',25));
+% figure('name','im_o','NumberTitle', 'off');imshow3D(im_o,[])
+bw_sub = zpic_DAPI - im_o;
+% figure('name','bw_sub','NumberTitle', 'off');imshow3D(bw_sub,[])
+
+%% THRESHOLDING
+thr=130;
+BW_Nuc=zpic_DAPI>thr; %Threshold each image separately?
+% figure('name','thresh','NumberTitle', 'off');imshow3Dfull(BW_Nuc,[])
+
+imcnt = size(zpic_DAPI, 3);
+
+% remove small particles
+bw_clean = zeros(size(BW_Nuc, 1), size(BW_Nuc, 2), imcnt);
+for i = 1:imcnt
+    bw_clean(:,:,i) = bwareaopen(BW_Nuc(:,:,i), 65);
+end
+% figure('name','open', 'NumberTitle','off');imshow3Dfull(bw_clean,[])
+
+label = bwlabeln(bw_clean);
+% figure('name','label', 'NumberTitle','off');imshow3Dfull(label,[])
+
+
+for cell_index=1:length(unique(label))-1
+  single_cell = zeros(size(label));
+  single_cell(find(label==cell_index))=1;
+  % figure('name','single_cell', 'NumberTitle','off');imshow3Dfull(single_cell,[])
+
+  idilate = imdilate(single_cell,strel('disk',5));
+  % figure('name','idilate', 'NumberTitle','off');imshow3Dfull(idilate,[])
+
+  stats = regionprops(idilate, 'BoundingBox');
+  bounding_box = [stats.BoundingBox];
+
+  x_min = bounding_box(1);
+  x_max = bounding_box(1) + bounding_box(4);
+  y_min = bounding_box(2);
+  y_max = bounding_box(2) + bounding_box(5);
+  z_periphery = 2; % number of z-slices above and below cell to display
+  z_min = round(bounding_box(3))-z_periphery;
+  z_max = round(bounding_box(3)) + bounding_box(6)+z_periphery;
+
+  if z_min < 1
+    z_min = 1;
+  end
+  if z_max > size(idilate,3);
+    z_max = size(idilate,3);
+  end
+
+  zdist = z_max - z_min;
+
+  cropped_cell = zeros(bounding_box(5)+1,bounding_box(4)+1,zdist);
+  transparency_map = zeros(bounding_box(5)+1,bounding_box(4)+1,zdist);
+  cropped_threshold = zeros(bounding_box(5)+1,bounding_box(4)+1,zdist);
+  %% Create image
+  i = 1;
+  for z=z_min:z_max-1
+    cropped_cell(:,:,i) = zpic_DAPI(y_min:y_max,x_min:x_max,z);
+    transparency_map(:,:,i) = idilate(y_min:y_max,x_min:x_max,z);
+    cropped_threshold(:,:,i) = single_cell(y_min:y_max,x_min:x_max,z);
+    i=i+1;
+  end
+
+  true_z_min = round(bounding_box(3));
+  true_z_max = round(bounding_box(3)) + bounding_box(6);
+  for z=1:z_periphery
+    if true_z_min - z > 0
+      transparency_map(:,:,z) = idilate(y_min:y_max,x_min:x_max,true_z_min);
+    end
+    if true_z_max + z <= size(idilate,3)
+      transparency_map(:,:,zdist + 1 - z) = idilate(y_min:y_max,x_min:x_max,true_z_max-1);
+    end
+  end
+
+  section = {};
+  section.title = ['Pancreatic Cell ID #' int2str(cell_index)];
+  images = [];
+
+
+  %% Display Image
+  figure('Position', [100, 100, 400, 1000]); hs = slice(cropped_cell,[],[],1:zdist);
+  shading interp; colormap hsv;
+  for n=1:length(hs) %% Apply transparency mask
+    hs(n).AlphaData = transparency_map(:,:,n);
+    hs(n).FaceAlpha = 'interp'; 
+  end
+  az = -68.7000;
+  el = 15.6000;
+  view(az,el);
+  saveas(gcf,['../public/img/HSV' int2str(cell_index) '.png'])
+  im.title = ['HSV'];
+  im.filename = ['HSV' int2str(cell_index) '.png'];
+  images = [images im];
+
+
+  %% Display Image
+  figure('Position', [100, 100, 400, 1000]); hs = slice(cropped_cell,[],[],1:zdist);
+  shading interp; colormap gray;
+  for n=1:length(hs) %% Apply transparency mask
+    hs(n).AlphaData = transparency_map(:,:,n);
+    hs(n).FaceAlpha = 'interp'; 
+  end
+  az = -68.7000;
+  el = 15.6000;
+  view(az,el);
+  saveas(gcf,['../public/img/Gray' int2str(cell_index) '.png'])
+  im.title = ['Gray'];
+  im.filename = ['Gray' int2str(cell_index) '.png'];
+  images = [images im];
+
+
+  %% Display Image
+  figure('Position', [100, 100, 400, 1000]); hs = slice(cropped_threshold,[],[],1:zdist);
+  shading interp; colormap hsv;
+  for n=1:length(hs) %% Apply transparency mask
+    hs(n).AlphaData = cropped_threshold(:,:,n);
+    hs(n).FaceAlpha = 'interp'; 
+  end
+  az = -68.7000;
+  el = 15.6000;
+  view(az,el);
+  saveas(gcf,['../public/img/Threshold' int2str(cell_index) '.png'])
+  im.title = ['Threshold'];
+  im.filename = ['Threshold' int2str(cell_index) '.png'];
+  images = [images im];
+
+  section.images = images;
+  data.sections = [data.sections section];
+  % break
+  % pause;
+  close all;
+  % if cell_index > 1
+  %   break
+  % end
+end
+
+addpath('jsonlab')
+savejson('',data,'FileName','data.json')
+fprintf('Finished.\n');