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ColiCell.m
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ColiCell.m
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classdef ColiCell < handle
properties
validCell
cellMask
topLeftX
topLeftY
parentSize
area
length
tilt
cheYMeanIntensity
cheZMeanIntensity
clusters
expansion
end
methods
function self = ColiCell( cellMask, tlx, tly, mIntensity,...
valid, sz, mIntensityZ, expansion )
self.cellMask = zeros( size( cellMask ) +...
( 2 * [ expansion expansion ] ) );
self.cellMask( expansion + 1:end - expansion,...
expansion + 1:end-expansion ) = cellMask;
self.validCell = valid;
self.topLeftX = ceil( tlx ) - expansion;
self.topLeftY = ceil( tly ) - expansion;
self.cheYMeanIntensity = mIntensity;
self.cheZMeanIntensity = mIntensityZ;
self.parentSize = sz;
self.expansion = expansion;
if self.validCell == 0
rp = regionprops( cellMask, 'Area',...
'MajorAxisLength', 'Orientation' );
self.area = rp.Area;
self.length = rp.MajorAxisLength;
self.tilt = rp.Orientation;
end
end
function mask = expandedMask( self )
mask = bwmorph( self.cellMask, 'dilate',...
floor( self.expansion / 1.5 ) );
end
function mask = fullMask( self )
mask = zeros( self.parentSize );
mask( self.topLeftY:self.topLeftY + size( self.cellMask, 1 ) - 1,...
self.topLeftX:self.topLeftX + size( self.cellMask, 2 ) - 1 )...
= self.cellMask;
end
function mask = expandedFullMask( self )
mask = zeros( self.parentSize );
mask( self.topLeftY:self.topLeftY + size( self.cellMask, 1 ) - 1,...
self.topLeftX:self.topLeftX + size( self.cellMask, 2 ) - 1 )...
= self.expandedMask();
end
function image = subImage( self, image )
image = image( self.topLeftY:self.topLeftY +...
size( self.cellMask, 1 ) - 1,...
self.topLeftX:self.topLeftX +...
size( self.cellMask, 2 ) - 1 );
end
function getClusters( self, image, cellBasalLevel, blackLevel,...
statSet, threshold, searchRadius, minSize, maxSize,...
xPix, yPix )
maskedImage = image .* self.expandedFullMask();
%figure(1);
%imshow( maskedImage, [min(maskedImage(:)), max(maskedImage(:))]);
self.clusters = {};
count = 0;
while(1)
ok = true;
[ maxPixelValue, maxPixelIndex ] = max( maskedImage(:) );
[ maxPixelY, maxPixelX ] = ind2sub( size(...
maskedImage ), maxPixelIndex );
if ( maxPixelValue < threshold * self.cheZMeanIntensity )
break
end
clusterBoxXMin = maxPixelX - searchRadius;
clusterBoxXMax = maxPixelX + searchRadius;
clusterBoxYMin = maxPixelY - searchRadius;
clusterBoxYMax = maxPixelY + searchRadius;
[ clusterBoxY, clusterBoxX ] = meshgrid(...
clusterBoxYMin:clusterBoxYMax,...
clusterBoxXMin:clusterBoxXMax );
clusterImage = image(...
clusterBoxYMin:clusterBoxYMax,...
clusterBoxXMin:clusterBoxXMax );
clusterBasalLevel = cellBasalLevel(...
clusterBoxYMin:clusterBoxYMax,...
clusterBoxXMin:clusterBoxXMax );
sumMass = sum( clusterImage(:) );
sumXMass = sum( sum( clusterBoxX .* clusterImage, 1 ), 2 );
sumYMass = sum( sum( clusterBoxY .* clusterImage, 1 ), 2 );
clusterCoMX = sumXMass / sumMass;
clusterCoMY = sumYMass / sumMass;
% CENTROID TO BE CENTERED ON CLUSTER
% centroid is given relative to maxPixelIndex always
centroidX = clusterCoMX - maxPixelX;
centroidY = clusterCoMY - maxPixelY;
beta = [ centroidX, centroidY, maxPixelValue * 1.5, 1 ];
xyInput = zeros( 1, numel( clusterImage ) );
zOutput = double( reshape( clusterImage -...
clusterBasalLevel - blackLevel,...
1, numel( clusterImage ) ) );
beta = nlinfit( xyInput, zOutput, @( beta, ~ )...
beta(3) * exp( -2 * ( ( xPix - beta(1) ) .^ 2 +...
( yPix - beta(2) ) .^ 2 ) /...
( beta(4) ) ^ 2 ), beta, statSet );
if beta(4) < minSize
ok = false;
end
if beta(4) > maxSize
ok = false;
end
if ok
count = count + 1;
self.clusters{ count } = ColiCluster(...
beta(1) + maxPixelX, beta(2) + maxPixelY,...
beta(3), beta(4) );
end
maskedImage(...
clusterBoxYMin:clusterBoxYMax,...
clusterBoxXMin:clusterBoxXMax ) = 0;
end
end
function cc = clusterCount( self )
cc = numel( self.clusters );
end
function cf = clusterFraction( self )
cf = zeros( 1, numel( self.clusters ) );
for i = 1:numel( self.clusters )
cf(i) = self.clusters{i}.fraction(...
self.cheZMeanIntensity, self.area );
end
end
end
end