From 9f5231e2bec15a06613bc4f6fe567aaa7de1805f Mon Sep 17 00:00:00 2001
From: Florian Vollrath <florian.vollrath@brain.mpg.de>
Date: Tue, 20 Sep 2016 11:26:10 +0200
Subject: [PATCH] deleted iterative shift correction and implemented cross
correlation
---
CellSortXCorr.m | 73 +++++++++++++++++++++++++++++++++++++
main.m | 33 +++++------------
readTiffNoStack.m | 4 ++
testOfDifferentTifImports.m | 32 ++++++++++++++++
4 files changed, 119 insertions(+), 23 deletions(-)
create mode 100644 CellSortXCorr.m
create mode 100644 readTiffNoStack.m
create mode 100644 testOfDifferentTifImports.m
diff --git a/CellSortXCorr.m b/CellSortXCorr.m
new file mode 100644
index 0000000..b065225
--- /dev/null
+++ b/CellSortXCorr.m
@@ -0,0 +1,73 @@
+function CellSortXCorr(nSubIm, nImages, m, n)
+% nSubIm = 10;
+% nImages = 1344;
+% m=14;
+% n=24;
+
+for k = m:n;
+ % Compose image stack from filenames
+ folder = sprintf('/storage/letz/Data/Data/Elisabeth_Abs/75EA/habituation/%u', k)
+ if exist(folder) == 0
+ continue
+ end
+ folder_corr = '/storage/letz/Data/Data/Elisabeth_Abs/75EA/habituation/corrected';
+
+ file_image_red = [folder, 'ChanB_0001_0001_0001_0001.tif'];
+ filePrefix_red = 'ChanB_0001_0001_0001_';
+
+ file_image_green = [folder, 'ChanA_0001_0001_0001_0001.tif'];
+ filePrefix_green = 'ChanA_0001_0001_0001_';
+
+ filename_red = sprintf([folder,filesep,filePrefix_red,'%04u.tif'],1);
+ im_red = imread(filename_red);
+
+ filename_green = sprintf([folder,filesep,filePrefix_green,'%04u.tif'],1);
+ im_green = imread(filename_green);
+
+ %preallocate data variable
+ allIm_red = zeros(size(im_red,1),size(im_red,2),nImages);
+ %read tiffs
+ for i = 1:nImages
+ filename_red = sprintf([folder,filesep,filePrefix_red,'%04u.tif'],i);
+ allIm_red(:,:,i) = readTiffNoStack(filename_red);
+ end
+
+ %preallocate data variable
+ allIm_green = zeros(size(im_green,1),size(im_green,2),nImages);
+ %read tiffs
+ for i = 1:nImages
+ filename_green = sprintf([folder,filesep,filePrefix_green,'%04u.tif'],i);
+ allIm_green(:,:,i) = readTiffNoStack(filename_green);
+ end
+
+
+ [rs, cs] = medAlign(allIm_red, nSubIm, 50, -inf);
+
+ registered = zeros(size(allIm_red,1),size(allIm_red,2),size(allIm_red,3), class(allIm_red));
+ parfor i = 1:nImages
+ registered(:,:,i) = circshift(allIm_red(:,:,i),[rs(i),cs(i)]);
+ end
+
+ data = binning(registered,[1,1,2],'mean');
+
+ filename = sprintf([folder_corr,filesep,'red_%u.tiff'],k);
+ for j=1:(nImages/2)
+ imwrite(uint16(data(:,:,j)),filename, 'tiff','WriteMode','append');
+ end
+
+
+
+ %align green channel with parameters from red alignment
+ parfor i = 1:nImages
+ registered(:,:,i) = circshift(allIm_green(:,:,i),[rs(i),cs(i)]);
+ end
+
+ data = binning(registered,[1,1,2],'mean');
+
+ filename = sprintf([folder_corr,filesep,'green_%u.tiff'],k);
+ for j=1:(nImages/2)
+ imwrite(uint16(data(:,:,j)),filename, 'tiff','WriteMode','append');
+ end
+
+
+end
\ No newline at end of file
diff --git a/main.m b/main.m
index 68810ae..9a4498b 100644
--- a/main.m
+++ b/main.m
@@ -1,29 +1,16 @@
-%% load and prepare all single tiffs
-%importing
-[data_g, data_r] = CellSortLoadSingleFiles('ChanA_*_*.tif', 'ChanB_*_*.tif');
-%% matVis
-matVis(data_r);
-%% get ref frame for shift correction
-interval = 1:20;
-refFrame = cast(mean(data_r(:,:,interval), 3), class(data_r));
-matVis(refFrame);
-%% shiftCorrection
-%generates shift corrected files for the green and red channels, needs
-%DIPlib (available for free)
-[data_g, data_r] = CellSortShiftCorrection(data_g, data_r, refFrame);
-%temporal binning
-binningFactor = [1 1 2]; %x, y, t
-[data_g, data_r] = CellSortTemporalBinning(data_g, data_r, binningFactor);
-
-fn = 'processedData.mat';
-save(fn, 'data_g', 'data_r', '-v7.3');
+%% load files and do cross correlation alignment
+nSubIm = 10;
+nImages = 1344;
+m=14;
+n=24;
+CellSortXCorr(nSubIm, nImages, m, n);
%% load files
-%if you haven't used the shiftCorrection you have to load the already processed files
-fn= 'processedData.mat';
-load(fn);
+fn_green = 'data_g.tif';
+fn_red = 'data_r.tif';
+data_g = readTiff(fn_green);
+data_r = readTiff(fn_red);
%% 1. PCA
%calculate PCAs
-fn_green = 'processedData.mat';
nPCs = 100;
flims = [];
dSamp = [1 1]; %temporal, spatial downsampling
diff --git a/readTiffNoStack.m b/readTiffNoStack.m
new file mode 100644
index 0000000..be515d5
--- /dev/null
+++ b/readTiffNoStack.m
@@ -0,0 +1,4 @@
+function data = readTiffNoStack(filename)
+t_g = Tiff(filename, 'r');
+data = t_g.read();
+end
\ No newline at end of file
diff --git a/testOfDifferentTifImports.m b/testOfDifferentTifImports.m
new file mode 100644
index 0000000..4e2fe42
--- /dev/null
+++ b/testOfDifferentTifImports.m
@@ -0,0 +1,32 @@
+fn = 'test.tif';
+
+tic;
+
+for i=1:5000
+data = readTiff(fn);
+end
+
+timeReadTiff = toc;
+
+tic;
+for i=1:5000
+data = imread(fn);
+end
+
+timeImread = toc;
+
+
+tic;
+for i=1:5000
+data = readTiffNoStack(fn);
+end
+
+timeNoStack = toc;
+
+tic;
+for i=1:5000
+t_g = Tiff(fn, 'r');
+data = t_g.read();
+end
+
+timeNoStackNoFunction = toc;
\ No newline at end of file