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fritsch
inPhase code repository
Commits
11d8ad95
Commit
11d8ad95
authored
2 years ago
by
fritsch
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Image segmentation/condensate_Segmentation_V4.m
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79 additions, 0 deletions
Image segmentation/condensate_Segmentation_V4.m
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11d8ad95
function
[
DataOut
,
maskDroplets
]
=
condensate_Segmentation_V4
(
imageCrop
,
emulsionMask
,
pixelSize
)
% in version 4 the watersheding was improved an switched on again
% calibrated for Olympus 40xUPLXAPO air objective at Olympus IX83 microscope
seSize
=
5
;
se
=
strel
(
'disk'
,
seSize
);
se2
=
strel
(
'disk'
,
20
);
% start image analysis
if
std2
(
imageCrop
)
<=
5
/
2
^
16
% no droplets in image
maskDroplets
=
0
;
else
% there are droplets start segmentation
% gradient based particle detection
imCropFilterd
=
roifilt2
(
imageCrop
,
emulsionMask
,
'imgaussfilt'
,
2
);
imCropFilterd
=
roifilt2
(
imCropFilterd
,
emulsionMask
,
'imgradient'
);
imCropFilterd
=
imCropFilterd
.
/
(
mean2
(
imCropFilterd
)
+
2
*
std2
(
imCropFilterd
));
imCropFilterd
(
imCropFilterd
<=
1
)
=
0
;
% bw treshholding step
thresh
=
adaptthresh
(
imCropFilterd
,
0.1
)
;
maskDroplets
=
imbinarize
(
imCropFilterd
,
thresh
);
% BW filtering
maskDroplets
=
imfill
(
maskDroplets
,
'holes'
);
maskDroplets
=
imerode
(
maskDroplets
,
se
);
% removes small objects (careful with se)
maskDroplets
=
bwareaopen
(
maskDroplets
,
seSize
);
% watershed to separate connected particles
% inspired by https://blogs.mathworks.com/steve/2013/11/19/watershed-transform-question-from-tech-support/
maskDist
=
-
bwdist
(
~
maskDroplets
);
maskDist2
=
imimposemin
(
maskDist
,
imextendedmin
(
maskDist
,
2
));
maskWatershed
=
watershed
(
maskDist2
);
maskDroplets
(
maskWatershed
==
0
)
=
0
;
maskDroplets
=
logical
(
maskDroplets
);
% derive solute mask and mean intensity
maskSolute
=
emulsionMask
-
imdilate
(
maskDroplets
,
se2
);
maskSolute
(
maskSolute
<
0
)
=
0
;
maskSolute
=
logical
(
imerode
(
maskSolute
,
se2
));
end
if
~
sum
(
sum
(
maskDroplets
))
==
0
dropletDiameters
=
regionprops
(
maskDroplets
,
'EquivDiameter'
);
dropletRadii
=
cat
(
1
,
dropletDiameters
.
EquivDiameter
)
.
/
2
.*
pixelSize
;
dropletVolumes
=
4
/
3
.*
pi
.*
dropletRadii
.^
3
;
dropletRegProps
=
regionprops
(
maskDroplets
,
imageCrop
,
'MeanIntensity'
,
'MaxIntensity'
,
'Eccentricity'
,
'Circularity'
,
'Centroid'
);
% Data output in case of condensates present
DataOut
.
dropletRadii
=
dropletRadii
;
DataOut
.
dropletVolumes
=
dropletVolumes
;
DataOut
.
dropletTotalVolume
=
sum
(
dropletVolumes
);
DataOut
.
dropletIntensities
=
[
dropletRegProps
.
MeanIntensity
]
'
;
DataOut
.
dropletIntensities_mean
=
mean
([
dropletRegProps
.
MeanIntensity
]);
DataOut
.
dropletIntensities_std
=
std
([
dropletRegProps
.
MeanIntensity
]);
DataOut
.
dropletIntensitiesMax
=
[
dropletRegProps
.
MaxIntensity
]
'
;
DataOut
.
dropletEccentricity
=
[
dropletRegProps
.
Eccentricity
]
'
;
DataOut
.
dropletCircularity
=
[
dropletRegProps
.
Circularity
]
'
;
DataOut
.
dropletCentroid
=
[
dropletRegProps
.
Circularity
]
'
;
DataOut
.
soluteIntensity_mean
=
mean
(
imageCrop
(
maskSolute
));
DataOut
.
soluteIntensity_std
=
std
(
imageCrop
(
maskSolute
));
else
% Data output in case of no condensates present
DataOut
.
dropletRadii
=
NaN
;
DataOut
.
dropletVolumes
=
NaN
;
DataOut
.
dropletTotalVolume
=
NaN
;
DataOut
.
dropletIntensities
=
NaN
;
DataOut
.
dropletIntensities_mean
=
NaN
;
DataOut
.
dropletIntensities_std
=
NaN
;
DataOut
.
dropletIntensitiesMax
=
NaN
;
DataOut
.
dropletEccentricity
=
NaN
;
DataOut
.
dropletCircularity
=
NaN
;
DataOut
.
dropletCentroid
=
NaN
;
DataOut
.
soluteIntensity_mean
=
mean
(
imageCrop
(
emulsionMask
));
DataOut
.
soluteIntensity_std
=
std
(
imageCrop
(
emulsionMask
));
end
end
\ No newline at end of file
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