Generating Bacteria Characteristics
Shape and Light Intensity
The light intensity of the bacteria was assumed to vary with a normal distribution across frames. The body of each bacteria had a homogenous light intensity, while the membrane was lighter in intensity than the cell body. The shape of the bacteria was also assumed to vary with a normal distribution across frames. It is evident from microscopy videos that the bacteria are rod shaped, and may appear to change shape as they tumble along the zaxis. The intensity of the membrane was assumed to be half the light intensity of that of the cell body.
MATLAB Code
%Generates Bacteria Shape and Color Intensity
function [bactshape,bactinten]=shape(nframes,dframe,L, W, SigSize, I, SigInt)
%Where L and W are the length and width of bacteria and I is the intensity.
%SigSize and SigInt are standard deviation in cell dimensions and intensity.
%nframes is the total number of frames and dframe is the frame step for which
%cell transition takse place. Total number of frames must be a multiple of frame step
%Determines Size of Array
i=1:dframe:nframes;
ShpSize=max(i)+dframe;
%Initialising Parameters
bactshape=zeros(ShpSize,3);
bactinten=zeros(ShpSize,1);
%Generate step characteristics
for n=1:dframe:ShpSize
bactshape(n,1)=abs(normrnd(L,SigSize));
bactshape(n,2)=abs(normrnd(W,SigSize));
bactshape(n,3)=randraw('vonmises',[0,1]);
%Ensures ColorSpec value to be from 0 to 1
if bactinten(n,1)>64  bactinten(n,2)>64
bactinten(n,1)=I;
bactinten(n,2)=I*2;
end;
end;
%Generating Bacteria Size and Color Intensity
for n=1:dframe:nframes
for i=(n+1):(n+dframe1)
bactshape(i,:)=bactshape(i1,:)+(bactshape(n+dframe,:)bactshape(n,:))/dframe;
bactinten(i,:)=bactinten(i1,:)+(bactinten(n+dframe,:)bactinten(n,:))/dframe;
end;
end;
%Returns Bacinten in the form of ColorSpec
bactinten=bactinten/64;
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