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updates after initial work on first drug screen islet
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| daniel/ | ||
| ResultTables/ | ||
| daniel/ignore | ||
| *.pptx | ||
| *.mat | ||
| ResultTables/ |
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| set(0,'DefaultFigureWindowStyle','docked') | ||
| inpath = '\\carbon.research.sickkids.ca\rkafri\YuvalDor\mouse islet z-stacks\images\3rd image set\Whole_mount_Islets_with_Torin_Cy5pdx_cy3E-cad_DAPI_080317'; | ||
| addpath '\\carbon.research.sickkids.ca\rkafri\Miriam\Matlab function library' | ||
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| %% 3rd set | ||
| % inpath = '\\carbon.research.sickkids.ca\rkafri\YuvalDor\mouse islet z-stacks\images\3rd image set\Whole_mount_Islets_with_Torin_Cy5pdx_cy3E-cad_DAPI_080317\'; | ||
| % folders = { | ||
| % '\Control\0003\' ... | ||
| % '\Control\0004\' ... | ||
| % '\Control\0005\' ... | ||
| % '\Torin\0000\' ... | ||
| % '\Torin\0001\' ... | ||
| % '\Torin\0002\' ... | ||
| % '\Torin_wash\0000\' ... | ||
| % '\Torin_wash\0001\' ... | ||
| % '\Torin_wash\0002\'}; | ||
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| %% First drug screened | ||
| inpath = '\\carbon.research.sickkids.ca\rkafri\YuvalDor\mouse islet z-stacks\images\Whole_mount_Mifepristone_Cy2pdx_Cy3Ecad_DAPI_080617\'; | ||
| folders = { | ||
| 'Control/Control/1_0_TIFF' ... | ||
| 'Control/Control/10001_TIFF' ... | ||
| 'Control/Control/10003_TIFF' ... | ||
| 'Control/Control/10004_TIFF' ... | ||
| 'Control/Control/10006_TIFF' ... | ||
| 'Control/Control/10007_TIFF' ... | ||
| 'Control/Control/10008_TIFF' ... | ||
| 'Control/Control/10009_TIFF' ... | ||
| 'Mifepristone_0.1nM/Mifepristone_0.1nM/1_TIFF' ... | ||
| 'Mifepristone_0.1nM/Mifepristone_0.1nM/1002_TIFF' ... | ||
| 'Mifepristone_0.1nM/Mifepristone_0.1nM/1004_TIFF' ... | ||
| 'Mifepristone_0.1nM/Mifepristone_0.1nM/1005_TIFF' ... | ||
| 'Mifepristone_0.1nM/Mifepristone_0.1nM/1006_TIFF' ... | ||
| 'Mifepristone_0.1nM/Mifepristone_0.1nM/1007_TIFF' ... | ||
| 'Mifepristone_10nM/Mifepristone_10nM/1_TIFF' ... | ||
| 'Mifepristone_10nM/Mifepristone_10nM/1_000_TIFF' ... | ||
| 'Mifepristone_10nM/Mifepristone_10nM/1_002_TIFF' ... | ||
| 'Mifepristone_10nM/Mifepristone_10nM/1_003_TIFF' ... | ||
| 'Mifepristone_10nM/Mifepristone_10nM/1_004_TIFF' ... | ||
| 'Mifepristone_10nM/Mifepristone_10nM/1_005_TIFF' ... | ||
| 'Mifepristone_1nM/Mifepristone_1nM/1_TIFF' ... | ||
| 'Mifepristone_1nM/Mifepristone_1nM/1001_TIFF' ... | ||
| 'Mifepristone_1nM/Mifepristone_1nM/1003_TIFF' ... | ||
| 'Mifepristone_1nM/Mifepristone_1nM/1004_TIFF' ... | ||
| 'Mifepristone_1nM/Mifepristone_1nM/1005_TIFF' ... | ||
| 'Mifepristone_1nM/Mifepristone_1nM/1006_TIFF'}; | ||
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| for f=1:length(folders) | ||
| folder = folders(f); | ||
| nuc = im3dread([inpath char(folder)], '*.tif', 1); % DAPI | ||
| cyto = im3dread([inpath char(folder)], '*.tif', 2); % e-cadherin | ||
| insulin = im3dread([inpath char(folder)], '*.tif', 3); % insulin? | ||
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| %% AUTO-CROP CYTO | ||
| padding = 30; % amount of padding around object to keep | ||
| big_blob = imdilate(cyto>0,strel('disk',5)); | ||
| big_blob = imopen(big_blob,strel('disk',40)); | ||
| stats = regionprops(big_blob, 'BoundingBox'); | ||
| assert(length(stats) == 1, 'Error: Auto-crop failed. Expected only one large blob in z-stack but found %d\n', length(stats)); | ||
| boundingbox = cat(1, stats.BoundingBox); | ||
| ymin = ceil(boundingbox(1)) - padding; | ||
| if ymin < 1 % out of bounds check | ||
| ymin = 1; | ||
| end | ||
| ymax = ceil(boundingbox(1)) + ceil(boundingbox(4)) + padding; | ||
| if ymax > size(cyto,1) % out of bounds check | ||
| ymax = size(cyto,1); | ||
| end | ||
| xmin = ceil(boundingbox(2)) - padding; | ||
| if xmin < 1 % out of bounds check | ||
| xmin = 1; | ||
| end | ||
| xmax = ceil(boundingbox(2)) + ceil(boundingbox(5)) + padding; | ||
| if xmax > size(cyto,2) % out of bounds check | ||
| xmax = size(cyto,2); | ||
| end | ||
| 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,[]); | ||
| %% CROP NUC | ||
| nuc=nuc(xmin:xmax,ymin:ymax,zmin:zmax); % crop; | ||
| % figure('name','nuc_cropped','NumberTitle', 'off'); imshow3D(nuc,[]); | ||
| %% CROP INSULIN | ||
| insulin=insulin(xmin:xmax,ymin:ymax,zmin:zmax); % crop | ||
| % figure('name','insulin_cropped','NumberTitle', 'off'); imshow3D(insulin,[]); | ||
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| nuc1 = nuc(:,:,2); % first | ||
| nuc2 = nuc(:,:,floor(size(nuc,3)/2)); % middle | ||
| nuc3 = nuc(:,:,end-1); % last | ||
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| cyto1 = cyto(:,:,2); % first | ||
| cyto2 = cyto(:,:,floor(size(cyto,3)/2)); % middle | ||
| cyto3 = cyto(:,:,end-1); % last | ||
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| insulin1 = insulin(:,:,2); % first | ||
| insulin2 = insulin(:,:,floor(size(insulin,3)/2)); % middle | ||
| insulin3 = insulin(:,:,end-1); % last | ||
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| label1 = text2im(int2str(2)); | ||
| label1 = imresize(label1 ,2); | ||
| insulin1(end-size(label1,1)+1:end,1:size(label1,2))=label1*255; % overlay text | ||
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| label2 = text2im(int2str(floor(size(insulin,3)/2))); | ||
| label2 = imresize(label2 ,2); | ||
| insulin2(end-size(label2,1)+1:end,1:size(label2,2))=label2*255; % overlay text | ||
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| label3 = text2im(int2str(size(insulin,3)-1)); | ||
| label3 = imresize(label3 ,2); | ||
| insulin3(end-size(label3,1)+1:end,1:size(label3,2))=label3*255; % overlay text | ||
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| all_nuc = [nuc1 nuc2 nuc3]; | ||
| all_cyto = [cyto1 cyto2 cyto3]; | ||
| all_insulin = [insulin1 insulin2 insulin3]; | ||
| all_images = [all_nuc; all_cyto; all_insulin]; | ||
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| folder_short = strrep(char(folder),'\','-'); | ||
| folder_short = strrep(char(folder),'/','-'); | ||
| folder_image = text2im(folder_short); | ||
| folder_image = imresize(folder_image ,2); | ||
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| % overlay folder name text text | ||
| all_images(1:size(folder_image,1),1:size(folder_image,2))=folder_image*255; | ||
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| % normalize between 0 and 255 | ||
| all_images = (all_images-min(all_images(:)))./(max(all_images(:))-min(all_images(:))).*255; | ||
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| % figure('name','nuc','NumberTitle', 'off'); imshow(all_images,[]); | ||
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| imwrite(uint8(all_images), ['overview_images_drug1/' folder_short '.png']); | ||
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| end |
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| <head> | ||
| <style> | ||
| </style> | ||
| </head> | ||
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| <img width="792" src="H:\Dropbox\Dropbox\Kafri\Projects\Islets\nuc_v2.gif"> | ||
| <img width="792" src="H:\Dropbox\Dropbox\Kafri\Projects\Islets\nuc_v5.gif"> | ||
| <img src="file:///D:/SickKids/DanielS/pancreatic_islets/GIFS/best/back_and_forth_Wash2_orig.gif"> | ||
| <img src="file:///D:/SickKids/DanielS/pancreatic_islets/GIFS/best/back_and_forth_Wash2.gif"> | ||
| <img class="thumb1" src="file:///D:/SickKids/DanielS/pancreatic_islets/GIFS/best/isosurface.gif"> | ||
| <video controls autoplay loop> | ||
| <source src="H:\Dropbox\Dropbox\Kafri\Projects\Islets\islet-supercut-v4.mp4" type="video/mp4"> | ||
| </video> | ||
| <!-- <img src="H:\Dropbox\Dropbox\Kafri\Projects\Islets\tablePicture1.png"> --> | ||
| <img src="D:\SickKids\BetaCellFigures\Nuc_v5_1.png"> | ||
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| <br> | ||
| <br> | ||
| <a href="H:\Dropbox\Dropbox\Kafri\Projects\Islets\pancreatic_islets_overview_images_Mifepristone.pptx"> | ||
| pancreatic_islets_overview_images_Mifepristone.pptx | ||
| </a> |
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