Tutorial for cell file manipulations

This tutorial shows some examples on how to use the cell files for your analysis.

Contents

Get location of the directory and the cell file folder

dirname = [filepath,'60mrnaCropped'];
cellFileFolder = [dirname, filesep,'xy1/cell'];

Load cell with ID 11

currentCell = load([cellFileFolder,filesep,'cell0000011.mat']);

% display the information in the cell file
currentCell

% print the motherID
disp (['mother id : ', num2str(currentCell.motherID)]);

% display the information at 12 frames after birth
disp('Cell Information at frame 12');
currentCell.CellA{12}

% show the foci scores at 12 frames after birth
disp('Foci scores at frame 12');
currentCell.CellA{12}.locus1(:).score

% information for the first focus
disp('First focus');
currentCell.CellA{12}.locus1(1)

% information for the second focus
disp('Second focus');
currentCell.CellA{12}.locus1(2)

currentCell = 

          CellA: {1x37 cell}
          death: 37
          birth: 1
         divide: 1
       sisterID: 0
       motherID: 0
     daughterID: [27 28]
             ID: 11
      neighbors: []
          stat0: 0
          ehist: 0
    contactHist: 0

mother id : 0
Cell Information at frame 12

ans = 

         cellLength: [32 8.7198]
                 xx: [1x41 double]
                 yy: [1x23 double]
               mask: [23x41 logical]
           r_offset: [266 217]
                 BB: [266 217 40 22]
           edgeFlag: 0
        contactHist: 0
       numNeighbors: 0
              phase: [23x41 uint16]
              coord: [1x1 struct]
             length: [32 13]
               pole: [1x1 struct]
             fluor1: [23x41 uint16]
           fluor1mm: [358 3610]
                fl1: [1x1 struct]
          cell_dist: 1
               gray: 5.4220e+03
             locus1: [1x2 struct]
    fluor1_filtered: [23x41 double]
                  r: [285.8996 227.6022]
              error: [1x1 struct]
              ehist: 0
              stat0: 0

Foci scores at frame 12

ans =

    6.9524


ans =

    3.9377

First focus

ans = 

                r: [298.8971 227.7778]
            score: 6.9524
        intensity: 11.0691
    normIntensity: 11.0691
        shortaxis: -1.9693
         longaxis: 12.8486
         fitSigma: 0.8483
         fitScore: 0.9444

Second focus

ans = 

                r: [283.5400 222.8604]
            score: 3.9377
        intensity: 6.1612
    normIntensity: 6.1612
        shortaxis: -4.2879
         longaxis: -3.1091
         fitSigma: 0.8401
         fitScore: 0.9517

Foci per frame

Make an array of number of foci per frame with score larger than 3 for this cell

frames = numel(currentCell.CellA);
fociPerFrame = zeros(1,frames);
for t = 1 : frames
    numFoci = numel(currentCell.CellA{t}.locus1);
    for i = 1 : numFoci
        if (currentCell.CellA{t}.locus1(i).score > 3)
            fociPerFrame(t) = fociPerFrame(t) + 1;
        end
    end
end

fociPerFrame

fociPerFrame =

  Columns 1 through 13

     1     1     1     1     1     1     2     2     1     1     1     2     1

  Columns 14 through 26

     1     1     1     2     2     1     2     1     2     1     1     0     3

  Columns 27 through 37

     3     2     2     2     2     2     2     2     1     1     2

Get cell files

allcells = dir([cellFileFolder,filesep '*ell*.mat'])
CompleteCellCylceCells = dir([cellFileFolder,filesep 'Cell*.mat'])

allcells = 

44x1 struct array with fields:

    name
    date
    bytes
    isdir
    datenum


CompleteCellCylceCells = 

4x1 struct array with fields:

    name
    date
    bytes
    isdir
    datenum

Count cells

Go through every cell file and count the number cells with at least one foci at birth above score 3

count = 0;
for i = 1 : numel(allcells)
    cellname = allcells(i).name;
    currentCell = load([cellFileFolder,filesep,cellname]);
    birth = 1;
    if isfield(currentCell.CellA{birth},'locus1') && currentCell.CellA{birth}.locus1(1).score>3
        count = count + 1;
    end

end

disp (['Cells with at least one foci with score > 3 : ', num2str(count)]);

Cells with at least one foci with score > 3 : 21

Average Cell Length

Go through every cell file, calculate the mean cell length, and make a histogram

% array of the average length for each cell
averageCellLengths = [];
for i = 1 : numel(allcells)
    cellname = allcells(i).name;
    currentCell = load([cellFileFolder,filesep,cellname]);

    % drill is a function that extracts a quantity from cellA for all time
    % frames
    lengthPerFrame = drill (currentCell.CellA, '.cellLength(1)');

    avCellLength = mean(lengthPerFrame);
    averageCellLengths(i) = avCellLength;
end

hist(averageCellLengths,5)

Published with MATLAB® R2016a