# IGEM:IMPERIAL/2008/Prototype/Drylab/Data Analysis/BSub Charac

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# 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 z-axis. 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+dframe-1)
bactshape(i,:)=bactshape(i-1,:)+(bactshape(n+dframe,:)-bactshape(n,:))/dframe;
bactinten(i,:)=bactinten(i-1,:)+(bactinten(n+dframe,:)-bactinten(n,:))/dframe;
end;
end;

%Returns Bacinten in the form of ColorSpec
bactinten=bactinten/64;

```