Make4DMatrix.m

seqPath = 'D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-11-15-Ai9CMAX PRotein Screen\Analysis\Baxter';
TrackVersion='_220106_115446';
FilePath=fullfile(seqPath,'Analysis',strcat('CellData',TrackVersion),'Compact');
a=dir(fullfile(FilePath,'*.mat'));
b={a.name};
HasCells=[a.bytes];
blank=~(HasCells>185);
d=b;
d(blank) =[];

for m=1:length(b)
    Run=b{1,m};
    Run=Run(1:end-4)
    if blank(m)
        BronkBox{1,1,1,m}={};    
    else
    cellPath=strcat(seqPath,'\',Run);
    cells = LoadCells(cellPath, TrackVersion, 'Compact', true);
    fluorProps = {cells.regionProps};
    fluorProps = cellfun(@fieldnames, fluorProps,'UniformOutput', false);
    fluorProps = unique(cat(1,fluorProps{:}))';
    BronkBox=cell(length(cells),max([cells.stopT]),length(fluorProps),NumWells);
for k=1:length(fluorProps)
    currProp=fluorProps{k};
    Test='MinorAxisLength';
for j=1:length(cells)
    c = cells(j);
    t = c.firstFrame : c.lastFrame;  
    tp=1;
    for i=t
        BronkBox{j,i,k,m}=cells(1,j).regionProps.(currProp)(tp);
        tp=tp+1;
    end
end
end
    end
end
empties=cellfun('isempty',BronkBox);
BronkBox(empties) = {NaN};
Data=cell2mat(BronkBox);
means=mean(Data(:,:,:,:),'omitnan');
medians=median(Data(:,:,:,:),'omitnan');
stds=std(Data(:,:,:,:),'omitnan');
vars=var(Data(:,:,:,:),'omitnan');
sums=sum(Data(:,:,:,:),'omitnan');
CVs=stds./means;