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demo_1p.m
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demo_1p.m
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% demo file for applying the NoRMCorre motion correction algorithm on
% 1-photon widefield imaging data
% Example file is provided from the miniscope project page
% www.miniscope.org
clear;
gcp;
%% download data and convert to single precision
name = 'msCam13.avi';
if ~exist(name,'file') % download file if it doesn't exist in the directory
url = 'https://caiman.flatironinstitute.org/~neuro/normcorre_datasets/msCam13.avi';
fprintf('downloading the file...');
outfilename = websave(name,url);
fprintf('done.');
end
%addpath(genpath('../../NoRMCorre'));
Yf = read_file(name);
Yf = single(Yf);
[d1,d2,T] = size(Yf);
%% perform some sort of deblurring/high pass filtering
if (0)
hLarge = fspecial('average', 40);
hSmall = fspecial('average', 2);
for t = 1:T
Y(:,:,t) = filter2(hSmall,Yf(:,:,t)) - filter2(hLarge, Yf(:,:,t));
end
%Ypc = Yf - Y;
bound = size(hLarge,1);
else
gSig = 7;
gSiz = 3*gSig;
psf = fspecial('gaussian', round(2*gSiz), gSig);
ind_nonzero = (psf(:)>=max(psf(:,1)));
psf = psf-mean(psf(ind_nonzero));
psf(~ind_nonzero) = 0; % only use pixels within the center disk
%Y = imfilter(Yf,psf,'same');
%bound = 2*ceil(gSiz/2);
Y = imfilter(Yf,psf,'symmetric');
bound = 0;
end
%% first try out rigid motion correction
% exclude boundaries due to high pass filtering effects
options_r = NoRMCorreSetParms('d1',d1-bound,'d2',d2-bound,'bin_width',200,'max_shift',20,'iter',1,'correct_bidir',false);
%% register using the high pass filtered data and apply shifts to original data
tic; [M1,shifts1,template1] = normcorre_batch(Y(bound/2+1:end-bound/2,bound/2+1:end-bound/2,:),options_r); toc % register filtered data
% exclude boundaries due to high pass filtering effects
tic; Mr = apply_shifts(Yf,shifts1,options_r,bound/2,bound/2); toc % apply shifts to full dataset
% apply shifts on the whole movie
%% compute metrics
[cY,mY,vY] = motion_metrics(Y(bound/2+1:end-bound/2,bound/2+1:end-bound/2,:),options_r.max_shift);
[cYf,mYf,vYf] = motion_metrics(Yf,options_r.max_shift);
[cM1,mM1,vM1] = motion_metrics(M1,options_r.max_shift);
[cM1f,mM1f,vM1f] = motion_metrics(Mr,options_r.max_shift);
%% plot rigid shifts and metrics
shifts_r = squeeze(cat(3,shifts1(:).shifts));
figure;
subplot(311); plot(shifts_r);
title('Rigid shifts','fontsize',14,'fontweight','bold');
legend('y-shifts','x-shifts');
subplot(312); plot(1:T,cY,1:T,cM1);
title('Correlation coefficients on filtered movie','fontsize',14,'fontweight','bold');
legend('raw','rigid');
subplot(313); plot(1:T,cYf,1:T,cM1f);
title('Correlation coefficients on full movie','fontsize',14,'fontweight','bold');
legend('raw','rigid');
%% now apply non-rigid motion correction
% non-rigid motion correction is likely to produce very similar results
% since there is no raster scanning effect in wide field imaging
options_nr = NoRMCorreSetParms('d1',d1-bound,'d2',d2-bound,'bin_width',50, ...
'grid_size',[128,128]*2,'mot_uf',4,'correct_bidir',false, ...
'overlap_pre',32,'overlap_post',32,'max_shift',20);
tic; [M2,shifts2,template2] = normcorre_batch(Y(bound/2+1:end-bound/2,bound/2+1:end-bound/2,:),options_nr,template1); toc % register filtered data
tic; Mpr = apply_shifts(Yf,shifts2,options_nr,bound/2,bound/2); toc % apply the shifts to the removed percentile
%% compute metrics
[cM2,mM2,vM2] = motion_metrics(M2,options_nr.max_shift);
[cM2f,mM2f,vM2f] = motion_metrics(Mpr,options_nr.max_shift);
%% plot shifts
shifts_r = squeeze(cat(3,shifts1(:).shifts));
shifts_nr = cat(ndims(shifts2(1).shifts)+1,shifts2(:).shifts);
shifts_nr = reshape(shifts_nr,[],ndims(Y)-1,T);
shifts_x = squeeze(shifts_nr(:,2,:))';
shifts_y = squeeze(shifts_nr(:,1,:))';
patch_id = 1:size(shifts_x,2);
str = strtrim(cellstr(int2str(patch_id.')));
str = cellfun(@(x) ['patch # ',x],str,'un',0);
figure;
ax1 = subplot(311); plot(1:T,cY,1:T,cM1,1:T,cM2); legend('raw data','rigid','non-rigid'); title('correlation coefficients for filtered data','fontsize',14,'fontweight','bold')
set(gca,'Xtick',[],'XLim',[0,T-3])
ax2 = subplot(312); plot(shifts_x); hold on; plot(shifts_r(:,2),'--k','linewidth',2); title('displacements along x','fontsize',14,'fontweight','bold')
set(gca,'Xtick',[])
ax3 = subplot(313); plot(shifts_y); hold on; plot(shifts_r(:,1),'--k','linewidth',2); title('displacements along y','fontsize',14,'fontweight','bold')
xlabel('timestep','fontsize',14,'fontweight','bold')
linkaxes([ax1,ax2,ax3],'x')
%% display downsampled data
tsub = 5;
Y_ds = downsample_data(Y,'time',tsub);
Yf_ds = downsample_data(Yf,'time',tsub);
M1_ds = downsample_data(M1,'time',tsub);
M1f_ds = downsample_data(Mr,'time',tsub);
M2_ds = downsample_data(M2,'time',tsub);
M2f_ds = downsample_data(Mpr,'time',tsub);
nnY_ds = quantile(Y_ds(:),0.0005);
mmY_ds = quantile(Y_ds(:),0.9995);
nnYf_ds = quantile(Yf_ds(:),0.0005);
mmYf_ds = quantile(Yf_ds(:),0.99995);
%%
make_avi = false; % save a movie
if make_avi
vidObj = VideoWriter('filtered.avi');
set(vidObj,'FrameRate',30);
open(vidObj);
end
fig = figure;
screensize = get(0,'Screensize' );
fac = min(min((screensize(3:4)-100)./[3*d2,d1]),10);
set(gcf, 'PaperUnits', 'points', 'Units', 'points');
set(gcf, 'Position', round([100 100 fac*3*d2 fac*d1]));
for t = 1:1:size(Y_ds,3)
if (0)
% plot filtered data
subplot(131);imagesc(Y_ds(:,:,t),[nnY_ds,mmY_ds]); xlabel('Raw data (downsampled)','fontsize',14,'fontweight','bold'); axis equal; axis tight;
colormap('bone');
set(gca,'XTick',[],'YTick',[]);
subplot(132);imagesc(M1_ds(:,:,t),[nnY_ds,mmY_ds]); xlabel('rigid corrected','fontsize',14,'fontweight','bold'); axis equal; axis tight;
title(sprintf('Frame %i out of %i',t,size(Y_ds,3)),'fontweight','bold','fontsize',14);
colormap('bone')
set(gca,'XTick',[],'YTick',[]);
subplot(133);imagesc(M2_ds(:,:,t),[nnY_ds,mmY_ds]); xlabel('non-rigid corrected','fontsize',14,'fontweight','bold'); axis equal; axis tight;
colormap('bone')
set(gca,'XTick',[],'YTick',[]);
else
% plot full data
subplot(131);imagesc(Yf_ds(:,:,t),[nnYf_ds,mmYf_ds]); xlabel('Raw data (downsampled)','fontsize',14,'fontweight','bold'); axis equal; axis tight;
colormap('bone');
set(gca,'XTick',[],'YTick',[]);
subplot(132);imagesc(M1f_ds(:,:,t),[nnYf_ds,mmYf_ds]); xlabel('rigid corrected','fontsize',14,'fontweight','bold'); axis equal; axis tight;
title(sprintf('Frame %i out of %i',t,size(Y_ds,3)),'fontweight','bold','fontsize',14);
colormap('bone')
set(gca,'XTick',[],'YTick',[]);
subplot(133);imagesc(M2f_ds(:,:,t),[nnYf_ds,mmYf_ds]); xlabel('non-rigid corrected','fontsize',14,'fontweight','bold'); axis equal; axis tight;
colormap('bone')
set(gca,'XTick',[],'YTick',[]);
end
drawnow;
if make_avi
currFrame = getframe(fig);
writeVideo(vidObj,currFrame);
end
end
if make_avi
close(vidObj);
end