Preprocessing: Motion Correction

Please use the online documentation website going forward: https://bahanonu.github.io/ciatah/

Scripts to register movies to remove motion.

Calculating final transformation after multiple registration iterations.

It is possible to use the output from motion correction (often done with turboregMovie or modelPreprocessMovieFunction) to transform the movie at later times if needed. There are two ways to do this:

• iteratively perform each motion correction step (e.g. same order as in modelPreprocessMovieFunction) or
• create the translation/skew/rotation matrices for each step using ResultsOutOriginal and combine for all iterations as totalTranformMatrix = (R2'*S2'*T2'*R1'*S1'*T1')'. Note the order matters.
  • Where 1, 2, ... indicate matrix for iterations 1,2,... and R, S, T are rotation, skew (shear + scale) and translation matrices, respectively.
  • For 3 iterations would be (R3'*S3'*T3'*R2'*S2'*T2'*R1'*S1'*T1')' or alternatively T1*S1*R1*T3*S3*R2*T3*S3*R3.
  • For translation/rotation matrices, use definitions in https://www.mathworks.com/help/images/matrix-representation-of-geometric-transformations.html to construct them.

Turboreg

Compiling turboreg and transfturboreg mex file

• Can compile on your system using the following command

mex('-v', '-largeArrayDims','-I.', 'turboreg.c','.\BsplnTrf.c','.\BsplnWgt.c','.\convolve.c','.\getPut.c','.\main.c','.\phil.c','.\pyrFilt.c','.\pyrGetSz.c','.\quant.c','.\reg0.c','.\reg1.c','.\reg2.c','.\reg3.c','.\regFlt3d.c','.\svdcmp.c')

mex('-v', '-largeArrayDims','-I.', 'transfturboreg.c','.\BsplnTrf.c','.\BsplnWgt.c','.\convolve.c','.\getPut.c','.\main.c','.\phil.c','.\pyrFilt.c','.\pyrGetSz.c','.\quant.c','.\reg0.c','.\reg1.c','.\reg2.c','.\reg3.c','.\regFlt3d.c','.\svdcmp.c')

• For Linux users: http://www.walkingrandomly.com/?p=2694

mex('-v', 'GCC="/usr/bin/gcc-4.9"', '-largeArrayDims','CFLAGS="\$CFLAGS -std=c99"','-I.', 'turboreg.c','./BsplnTrf.c','./BsplnWgt.c','./convolve.c','./getPut.c','./main.c','./phil.c','./pyrFilt.c','./pyrGetSz.c','./quant.c','./reg0.c','./reg1.c','./reg2.c','./reg3.c','./regFlt3d.c','./svdcmp.c')

mex('-v', 'GCC="/usr/bin/gcc-4.9"', '-largeArrayDims','CFLAGS="\$CFLAGS -std=c99"','-I.', 'transfturboreg.c','./BsplnTrf.c','./BsplnWgt.c','./convolve.c','./getPut.c','./main.c','./phil.c','./pyrFilt.c','./pyrGetSz.c','./quant.c','./reg0.c','./reg1.c','./reg2.c','./reg3.c','./regFlt3d.c','./svdcmp.c')

• Below is an example usage of turboregMovie.
• To use imageJ in Matlab, download Fiji (http://fiji.sc) and add Miji.m to your filepath, see http://fiji.sc/Miji.

Running turboreg

Note this input was from 2017.04.19 update

% set turboreg options
ioptions.inputDatasetName = '/1';
ioptions.turboregRotation = 0;
ioptions.RegisType = 1;
ioptions.parallel = 1;
ioptions.meanSubtract = 1;
ioptions.normalizeType = 'bandpass'; % matlabDisk is alternative input. Done on input to turboreg but NOT on final movie.
ioptions.registrationFxn = 'transfturboreg';
ioptions.normalizeBeforeRegister = 'divideByLowpass'; % set to blank if don't want any filtering on output movie
ioptions.imagejFFTLarge = 10000;
ioptions.imagejFFTSmall = 80;
ioptions.saveNormalizeBeforeRegister = [];
ioptions.cropCoords = [];
ioptions.closeMatlabPool = 0;
ioptions.refFrame = 1;
ioptions.refFrameMatrix = [];

% load the movie and run turboreg
inputMovieMatrix = loadMovieList('data\2014_04_01_p203_m19_check01\concat_recording_20140401_180333.h5');
regMovie = turboregMovie(inputMovieMatrix,'options',ioptions);

% or run turboreg function by loading movie directly within function
regMovie = turboregMovie('pathToDir\filename.h5','options',ioptions);

Old input

ioptions.inputDatasetName = '/1';
ioptions.turboregRotation = 1;
ioptions.RegisType = 1;
ioptions.parallel = 1;
ioptions.meanSubtract = 1;
ioptions.normalizeType = 'divideByLowpass';
ioptions.registrationFxn = 'transfturboreg';
ioptions.normalizeBeforeRegister = 'imagejFFT';
ioptions.imagejFFTLarge = 10000;
ioptions.imagejFFTSmall = 80;
ioptions.saveNormalizeBeforeRegister = [];
ioptions.cropCoords = [];
ioptions.closeMatlabPool = 0;
ioptions.refFrame = 1;
ioptions.refFrameMatrix = [];
regMovie = turboregMovie('pathToDir\filename.h5','options',ioptions);
% OR
regMovie = turboregMovie(inputMovieMatrix,'options',ioptions);