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mpibr
scic
NeuroBits
Commits
77a7c088
Commit
77a7c088
authored
8 years ago
by
Georgi Tushev
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fix to absolute units of puncta intensity
parent
6159eaca
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1 changed file
utils/countPunctaInNeuroTrees.m
+7
-3
7 additions, 3 deletions
utils/countPunctaInNeuroTrees.m
with
7 additions
and
3 deletions
utils/countPunctaInNeuroTrees.m
+
7
−
3
View file @
77a7c088
...
@@ -7,7 +7,7 @@ close all
...
@@ -7,7 +7,7 @@ close all
%% --- THINGS TO CHANGE BEFORE RUN --- %%
%% --- THINGS TO CHANGE BEFORE RUN --- %%
%% --- input parameters --- %%
%% --- input parameters --- %%
channelPuncta
=
2
;
channelPuncta
=
2
;
dataPath
=
'/Users/
lisakochen
/Desktop/3
31
/'
;
dataPath
=
'/Users/
tushevg
/Desktop/3
29
/'
;
minPunctaSize
=
2
;
minPunctaSize
=
2
;
minPeakRatio
=
0.18
;
minPeakRatio
=
0.18
;
nhood
=
13
;
% [pixels] from branch center to closest puncta
nhood
=
13
;
% [pixels] from branch center to closest puncta
...
@@ -100,6 +100,9 @@ close all
...
@@ -100,6 +100,9 @@ close all
% sum projection
% sum projection
prj
=
sum
(
double
(
img
),
3
);
prj
=
sum
(
double
(
img
),
3
);
% mean projection
prj_avg
=
mean
(
img
,
3
);
% apply spatial filter
% apply spatial filter
prj
=
imgaussfilt
(
prj
,
0.5
,
'Padding'
,
'symmetric'
);
prj
=
imgaussfilt
(
prj
,
0.5
,
'Padding'
,
'symmetric'
);
...
@@ -111,9 +114,10 @@ close all
...
@@ -111,9 +114,10 @@ close all
bry
=
(
prj
==
dil
)
&
(
prj
>
minPeakRatio
);
bry
=
(
prj
==
dil
)
&
(
prj
>
minPeakRatio
);
% get weighted centroid
% get weighted centroid
props
=
regionprops
(
bry
,
dil
,
'WeightedCentroid'
,
'MeanIntensity'
);
props
=
regionprops
(
bry
,
dil
,
'WeightedCentroid'
);
props_ity
=
regionprops
(
bry
,
prj_avg
,
'MeanIntensity'
);
weightedCentroids
=
round
(
cat
(
1
,
props
.
WeightedCentroid
));
weightedCentroids
=
round
(
cat
(
1
,
props
.
WeightedCentroid
));
punctaMeanIntensity
=
double
(
cat
(
1
,
props
.
MeanIntensity
));
punctaMeanIntensity
=
double
(
cat
(
1
,
props
_ity
.
MeanIntensity
));
punctaCount
=
size
(
weightedCentroids
,
1
);
punctaCount
=
size
(
weightedCentroids
,
1
);
punctaIndex
=
sub2ind2D
(
range
,
weightedCentroids
(:,
2
),
weightedCentroids
(:,
1
));
punctaIndex
=
sub2ind2D
(
range
,
weightedCentroids
(:,
2
),
weightedCentroids
(:,
1
));
...
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