Some of the starting code for exercises related to the Single Object Analysis

Shape Analysis with FIJI

% start Fiji interface
cur_dir=pwd;
Miji
% for some reason the miji script changes directory so this changes it back
cd(cur_dir); 
% create the simulated image
[outImage,out_pos,out_shape,out_theta] = cell_simulator(100,10,3,0,1);
% send the image to FIJI
MIJ.createImage('test',outImage,true);
% set a threshold (yes the programmer spelled it incorrectly)
MIJ.setTreshold(0,253);
% convert the image to a binary image using the threshold
MIJ.run('Convert to Mask')
% invert the lookup table (LUT) so that black is 0 and white is 255
MIJ.run('Invert LUT');
% Use the Analyze Particles feature to count the objects
MIJ.run('Invert'); % it requires an inverted image (objects are 0, holes are 255)
MIJ.run('Set Measurements...', 'area centroid perimeter bounding fit shape stack redirect=None decimal=3');
MIJ.run('Analyze Particles...', 'show=Ellipses display clear');
% Get the names of the output
shapeColNames=MIJ.getListColumns;
% Get the results table
shapeAnalysis=MIJ.getResultsTable;
% get the area column from the shape analysis
analysisArea=shapeAnalysis(:,1);
% calculate the histograms for the final area distribution
[inCounts,inAreas]=hist(pi*out_shape(:,1).*out_shape(:,2));
[outCounts,outAreas]=hist(shapeAnalysis(:,1),inAreas);
% close all the other windows
close all
% plot the histograms in figure 1
figure(1)
plot(inAreas,inCounts,'r-',outAreas,outCounts,'b-')
legend({'Model Areas','Calculated Areas'})
xlabel('Pixel Count')
ylabel('Cell Count')
% show the positions in figure 2
figure(2)
plot(out_pos(:,1),out_pos(:,2),'r.',shapeAnalysis(:,2),shapeAnalysis(:,3),'b+')
legend({'Model Position','Calculated Position'})
xlabel('X Position')
ylabel('Y Position')