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synapto_display.m
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synapto_display.m
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% This script imports individual synaptosome images and displaying them in
% a montage with their labels. The script looks for the cropped 8-bit
% visualizations of individual synaptosomes output by compareConditions.m
% with images for three different fluorescent channels, and displays them
% in a montage with an overlay of the three channels and the label for the
% synaptosome ID.
% Ancillary functions:
% GetImages.m
% natsortfiles.m
% imdisp.m (Copyright (c) 2010, Oliver Woodford. All rights reserved.)
% Author: Pedro Vallejo Ramirez [email protected]
% Laser Analytics Group
% Updated 28/09/2018
%% Load raw synaptosome reconstructions
close all
Path = 'E:\Experiments\synaptosomes\analysis_20190107\37C_results_thresh30\Results_combined\Repeat_B\ripley\phys\images';
output_dir = 'E:\Experiments\synaptosomes\analysis_20190107\37C_results_thresh30\Results_combined';
% load .csv file with trimmed pooled results after manual removal of "ugly"
% regions
csv_path = "E:\Experiments\synaptosomes\analysis_20190107\4C_results\Results_combined\results_combined_pooled_trimmed.csv";
results_pooled = resultscombinedpooledtrimmed;
% select area token and label token for your data files
condition = 'phys';
repeat = 'B';
im_cutoff = 20;
show = 0;
RC_token = ['_' condition '_RC_synaptosome_'];
GC_token = ['_' condition '_GC_synaptosome_'];
BC_token = ['_' condition '_BC_synaptosome_'];
[PathNameRC, FileNames_RC] = GetImages(Path, RC_token );
[PathNameGC, FileNames_GC] = GetImages(Path, GC_token );
[PathNameBC, FileNames_BC] = GetImages(Path, BC_token );
N_files = size(FileNames_RC,1);
disp('------------------------------------------------');
disp('------------------------------------------------');
disp('Opening files in following folder:');
disp(PathNameRC);
disp(['Number of files found: ', num2str(N_files)]);
% choose names from relevant repeat and condition
sampleIDs_repeat = results_pooled(strcmp(results_pooled.Repeat,repeat),:);
sampleIDs_condition = sampleIDs_repeat(strcmp(sampleIDs_repeat.condition,condition),:);
num_trimmed_files = size(sampleIDs_condition);
sampleIDs_names = cell(num_trimmed_files(1),1);
% concatenate names of sample ID and synaptosome ID
for i = 1:num_trimmed_files(1)
temp = strsplit(sampleIDs_condition.sampleID(i),'_');
samp_ID = strcat(temp(1)," ",temp(2));
sampleIDs_names{i,1} = strcat(samp_ID," " ,num2str(sampleIDs_condition.synaptosomeID(i)));
end
%% display images
imred = cell(N_files,1);
imgreen = cell(N_files,1);
imblue = cell(N_files,1);
overlay = cell(N_files,1);
red = cell(N_files,1);
green = cell(N_files,1);
blue = cell(N_files,1);
imlabel = cell(N_files,1);
im_names = cell(N_files,1);
trimmed_names_indices = false(N_files,1);
path_output = fullfile(output_dir, filesep,['Synapto_montage_' condition repeat ]);
if exist(path_output, 'dir')
opts.Interpreter = 'tex';
opts.Default = 'Continue';
quest = '\fontsize{12}An output folder ''Results'' already exists. If you continue, data in this folder might be overwritten.';
answer = questdlg(quest,'Message','Cancel','Continue',opts);
if strcmp(answer,'Continue')
mkdir(path_output);
else
return
end
else
mkdir(path_output);
end
for i = 1: N_files
% read in images and transform into RGB to get a colormap for each
imred{i,1} = imread(FileNames_RC{i});
imgreen{i,1} = imread(FileNames_GC{i});
imblue{i,1} = imread(FileNames_BC{i});
im_size = size(imred{1,1});
overlay{i,1} = cat(3,imred{i,1},imgreen{i,1},imblue{i,1});
red{i,1} = cat(3,imred{i,1},zeros(size(imred{i,1})),zeros(size(imred{i,1})));
green{i,1} = cat(3,zeros(size(imred{i,1})),imgreen{i,1},zeros(size(imred{i,1})));
blue{i,1} = cat(3,zeros(size(imred{i,1})),zeros(size(imred{i,1})),imblue{i,1});
% write out labels for each image
imlabel{i,1} = ones(im_size(1),im_size(1));
im_size2 = size(imlabel{i,1});
[filepath,name,ext] = fileparts(FileNames_RC{i});
string_length = strlength(name);
string = strsplit(name,'_');
im_names{i,1} = [string{1} ' ' string{2} ' ' string{5}];
position = [im_size2(2)/2 im_size2(1)/2];
imlabel{i,1} = insertText(imlabel{i,1},position,im_names{i,1},'AnchorPoint','Center','TextColor','black','FontSize',16,'BoxColor','white');
imlabel{i,1} = rot90(imlabel{i,1});
% now choose only images with labels which correspond to labels on the
% trimmed spreadsheet
for lp = 1:num_trimmed_files(1)
same = strcmp(im_names{i,1},sampleIDs_names{lp});
if same
trimmed_names_indices(i) = true;
end
end
end
% Keep only images which correspond to selected ones on the trimmed
% spreadsheet
red = red(trimmed_names_indices,:);
green = green(trimmed_names_indices,:);
blue = blue(trimmed_names_indices,:);
overlay = overlay(trimmed_names_indices,:);
imlabel = imlabel(trimmed_names_indices,:);
N_files = size(red,1);
% cycle through the images, 20 at a time, display them, and then continue
% with the next 20 until there are none left
% divide arrays into sub-arrays with 20 images each
remainder = mod(N_files,im_cutoff);
if remainder >0
num_sub_arrays = floor(N_files/im_cutoff)+1;
else
num_sub_arrays = floor(N_files/im_cutoff);
end
count = 1;
if num_sub_arrays == 1
remainder = N_files;
end
for j = 1:num_sub_arrays
% only on the last count of the loop, if the mod is more than 0, fix
if j == num_sub_arrays % on the last run of the loop, run until the end of the number of files
red_j(1:remainder,1) = red(count:N_files,1);
green_j(1:remainder,1) = green(count:N_files,1);
blue_j(1:remainder,1) = blue(count:N_files,1);
overlay_j(1:remainder,1) = overlay(count:N_files,1);
imlabel_j(1:remainder,1) = imlabel(count:N_files,1);
h=figure;imdisp([red_j green_j blue_j overlay_j imlabel_j],'Size',[5 remainder],'Border',0.02)
else
red_j(1:im_cutoff,1) = red(count:j*im_cutoff,1);
green_j(1:im_cutoff,1) = green(count:j*im_cutoff,1);
blue_j(1:im_cutoff,1) = blue(count:j*im_cutoff,1);
overlay_j(1:im_cutoff,1) = overlay(count:j*im_cutoff,1);
imlabel_j(1:im_cutoff,1) = imlabel(count:j*im_cutoff,1);
count = count+im_cutoff;
h=figure;imdisp([red_j green_j blue_j overlay_j imlabel_j],'Size',[5 im_cutoff],'Border',0.02)
end
% export figure to a pdf for display
set(h,'Units','Inches');
pos = get(h,'Position');
set(h,'PaperPositionMode','Auto','PaperUnits','Inches','PaperSize',[pos(3), pos(4)])
filename = [condition '_synapto_montage_' num2str(j)];
print(h,[path_output filesep filename],'-dpdf','-r300')
clear red_j green_j blue_j overlay_j imlabel_j
end
% Display image montage
%figure;imdisp([red green blue overlay imlabel],'Size',[5 N_files],'Border',0.02)
%
% for j = 1:num_sub_arrays
% % only on the last count of the loop, if the mod is more than 0, fix
% if j == num_sub_arrays % on the last run of the loop, run until the end of the number of files
% red_j(count:N_files,1) = red(count:N_files,1);
% green_j(count:N_files,1) = green(count:N_files,1);
% blue_j(count:N_files,1) = blue(count:N_files,1);
% else
% red_j(count:j*im_cutoff,1) = red(count:j*im_cutoff,1);
% green_j(count:j*im_cutoff,1) = green(count:j*im_cutoff,1);
% blue_j(count:j*im_cutoff,1) = blue(count:j*im_cutoff,1);
% count = count+im_cutoff;
% end
%
% figure;imdisp([red_j green_j blue_j ],'Size',[3 im_cutoff],'Border',0.02)
% end
%