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| | <div id="find-collapse" class="panel-collapse collapse" role="tabpanel" aria-labelledby="find"> | | <div id="find-collapse" class="panel-collapse collapse" role="tabpanel" aria-labelledby="find"> |
| | <div class="panel-body"> | | <div class="panel-body"> |
| − | | + | <img class="img-responsive" src="https://static.igem.org/mediawiki/2017/1/1b/T--oxford--measurement--matlabcode.jpeg"> |
| − | <p>imgname = ''; %input image name between quotes(e.g. 'img_name.tif') | + | |
| − | | + | |
| − | A = imread(imgname);
| + | |
| − | | + | |
| − | fprintf('------ Image: %s ------\n', imgname);
| + | |
| − | | + | |
| − | x_size = size(A,2);
| + | |
| − | y_size = size(A,1);
| + | |
| − | | + | |
| − | A = A * 30;
| + | |
| − | phase = A(:,:,3);
| + | |
| − | data = A(:,:,2);
| + | |
| − | | + | |
| − | | + | |
| − | s_test = 0.52:0.005:0.575;
| + | |
| − | results = zeros(1,length(s_test));
| + | |
| − | | + | |
| − | figure;
| + | |
| − | | + | |
| − | for n = -1%[1:length(s_test) -1]
| + | |
| − | if n ~= -1
| + | |
| − | s = s_test(n);
| + | |
| − | else
| + | |
| − | s = 0.55;%input('Enter best sensitivity: ');
| + | |
| − | end
| + | |
| − | a_thresh = adaptthresh(phase,s);
| + | |
| − | cells = imbinarize(phase, a_thresh);
| + | |
| − | cells = imerode(cells, strel('disk',2,4));
| + | |
| − | cells = imdilate(cells, strel('disk',6,8));
| + | |
| − | nw_line = zeros(5,5);
| + | |
| − | nw_line(3,3) = 1;
| + | |
| − | nw_line(4,4) = 1;
| + | |
| − | nw_line(
| + | |
| − | cells = conv2(cells,
| + | |
| − |
| + | |
| − | Remove extremely bright spots
| + | |
| − | cells(data > 3000) = 0;
| + | |
| − |
| + | |
| − | Remove small "cells"
| + | |
| − | cells = bwareaopen(cells,500);
| + | |
| − |
| + | |
| − | cells_red = zeros(y_size,x_size,3);
| + | |
| − | cells_red(:,:,1) = cells;
| + | |
| − |
| + | |
| − | [gx, gy] = gradient(single(phase));
| + | |
| − | gmax = max(max(gx(:)),max(gy(:)));
| + | |
| − | gmag = sqrt(gx.^2 + gy.^2);
| + | |
| − | gmask = (gmag/gmax) > 0.05;
| + | |
| − | gmask = bwareaopen(gmask, 800);
| + | |
| − | gmask = imclose(gmask,strel('disk',5));
| + | |
| − | gmask = imerode(gmask,strel('disk',5));
| + | |
| − | gmask = imdilate(gmask,strel('disk',3));
| + | |
| − | gmask = imerode(gmask,strel('disk',10));
| + | |
| − | gmask = imdilate(gmask,strel('disk',10));
| + | |
| − | gmask = bwareaopen(gmask, 1000);
| + | |
| − | gmask(data > 3000) = 0;
| + | |
| − | gmask_green = zeros(y_size,x_size,3);
| + | |
| − | gmask_green(:,:,2) = gmask;
| + | |
| − | | + | |
| − | if n ~= -1
| + | |
| − | subplot(3,4,n);
| + | |
| − | hold on;
| + | |
| − | imagesc(phase);
| + | |
| − | image('CData', cells_red, 'AlphaData', cells*0.3);
| + | |
| − | axis ij;
| + | |
| − | axis tight;
| + | |
| − | title(sprintf('s = %5.3f', s));
| + | |
| − | colormap gray;
| + | |
| − | end;
| + | |
| − | end;
| + | |
| − | | + | |
| − | clf;
| + | |
| − | | + | |
| − | Auto-alignment didn't really work
| + | |
| − | combined = logical(cells);
| + | |
| − | crr_full = xcorr2(single(data), single(combined));
| + | |
| − | crr = crr_full(((1:y_size) + floor(y_size/2)), ((1:x_size) + floor(x_size/2)));
| + | |
| − | [max_crr, max_crr_i] = max(crr(:));
| + | |
| − | [max_crr_y, max_crr_x] = ind2sub(size(crr),max_crr_i);
| + | |
| − | x_offset = (max_crr_x) - (x_size/2);
| + | |
| − | y_offset = (max_crr_y) - (y_size/2);
| + | |
| − | | + | |
| − | x_sclip = (x_offset > 0) * abs(x_offset) + (x_offset <= 0);
| + | |
| − | x_eclip = (x_offset < 0) * abs(x_offset) + (x_offset >= 0);
| + | |
| − | y_sclip = (y_offset > 0) * abs(y_offset) + (y_offset <= 0);
| + | |
| − | y_eclip = (y_offset < 0) * abs(y_offset) + (y_offset >= 0);
| + | |
| − | | + | |
| − | mask_offset = zeros(y_size,x_size);
| + | |
| − | mask_offset(y_sclip:(y_size-y_eclip),x_sclip:(x_size-x_eclip)) = ...
| + | |
| − | combined(y_eclip:(y_size-y_sclip),x_eclip:(x_size-x_sclip));
| + | |
| − | | + | |
| − | mask_offset = combined;
| + | |
| − | | + | |
| − | cells_green = zeros(y_size,x_size,3);
| + | |
| − | cells_green(:,:,2) = cells_offset;
| + | |
| − | | + | |
| − | cell_flr = mean(data(mask_offset == 1));
| + | |
| − | cell_flr_std = std(single(data(mask_offset == 1)));
| + | |
| − | bg_flr = mean(data(mask_offset == 0));
| + | |
| − | bg_flr_std = std(single(data(mask_offset == 0)));
| + | |
| − | | + | |
| − | fprintf('Cell Detection Sensitivity : %7.2f\n', s);
| + | |
| − | fprintf('Automatic Mask Offset : (%+3d, %+3d)\n', x_offset, y_offset);
| + | |
| − | fprintf('Cell Fluoresence : %7.2f +/- %7.2f\n', cell_flr, cell_flr_std);
| + | |
| − | fprintf('Background Fluorescence : %7.2f +/- %7.2f\n', bg_flr, bg_flr_std);
| + | |
| − | fprintf('Blank Adjusted Fluoresence : %7.2f +/- %7.2f\n', cell_flr - bg_flr, sqrt(cell_flr_std^2 + bg_flr_std^2));
| + | |
| − | | + | |
| − | hold on;
| + | |
| − | | + | |
| − | subplot(3,2,[1 3]);
| + | |
| − | imagesc(phase);
| + | |
| − | image('CData', cells_red, 'AlphaData', cells*0.2);
| + | |
| − | image('CData', gmask_green, 'AlphaData', gmask*0.2);
| + | |
| − | axis ij;
| + | |
| − | axis tight;
| + | |
| − | title('Cells Image');
| + | |
| − | colormap gray;
| + | |
| − | | + | |
| − | subplot(3,2,5);
| + | |
| − | [cells_label, total_cells] = bwlabeln(cells);
| + | |
| − | cell_area = zeros(1,total_cells);
| + | |
| − | for c = 1:total_cells
| + | |
| − | cell_area(c) = bwarea(cells_label == c);
| + | |
| − | end
| + | |
| − | histogram(cell_area,20,'EdgeColor','k','FaceColor','k');
| + | |
| − | title('"Cell" Size Histogram');
| + | |
| − | | + | |
| − | subplot(3,2,[2 4]);
| + | |
| − | hold on;
| + | |
| − | imagesc(data);
| + | |
| − | image('CData', cells_red, 'AlphaData', cells*0.2);
| + | |
| − | image('CData', gmask_green, 'AlphaData', gmask*0.2);
| + | |
| − | axis ij;
| + | |
| − | axis tight;
| + | |
| − | title('Data Image');
| + | |
| − | set(gca, 'CLim', [800 1400]);
| + | |
| − | colormap gray;
| + | |
| − | | + | |
| − | subplot(3,2,6);
| + | |
| − | hold on;
| + | |
| − | histogram(data(logical((cells == 0) .* (gmask == 0))),50,'EdgeColor','k','FaceColor','k','Normalization','probability','BinLimits',[0 2000]);
| + | |
| − | histogram(data(cells == 1),50,'EdgeColor','k','FaceColor','r','Normalization','probability','BinLimits',[0 2000]);
| + | |
| − | histogram(data(gmask == 1),50,'EdgeColor','k','FaceColor','g','Normalization','probability','BinLimits',[0 2000]);
| + | |
| − | histogram(data(logical((cells == 1) + (gmask == 1))),50,'EdgeColor','k','FaceColor','y','Normalization','probability','BinLimits',[0 2000]);
| + | |
| − | title('Data Image Histogram');
| + | |
| − | colormap gray;
| + | |
| − | | + | |
| − | | + | |
| − | subplot(3,3,[2 5]);
| + | |
| − | hold on;
| + | |
| − | imagesc(crr);
| + | |
| − | plot([x_size/2 max_crr_x], [y_size/2 max_crr_y], 'r-');
| + | |
| − | axis ij;
| + | |
| − | axis tight;
| + | |
| − | title('2D Cross Correlation of Data with Cells Position');
| + | |
| − | colormap gray;
| + | |
| − | </p>
| + | |
| | | | |
| | </div> | | </div> |
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| | </div> | | </div> |
| | | | |
| | + | <img class = "img-responsive img-center" src = "https://static.igem.org/mediawiki/2017/6/61/T--oxford--measurement--demo.png"></img> |
| | + | <h6>Figure 1. An Example of the Measurement Program Applied to One of Our Microscope Images</h6> |
| | | | |
| | | | |
| − | | + | </div> |
| | </div> | | </div> |
| | </body> | | </body> |
