computeFeatures: Compute object features
In EBImage: Image processing and analysis toolbox for R
Description
Usage
Arguments
Details
Value
Author(s)
References
See Also
Examples
View source: R/computeFeatures.R
Description
Computes morphological and texture features from image objects.
Usage
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computeFeatures(x, ref, methods.noref=c("computeFeatures.moment", "computeFeatures.shape"),
methods.ref=c("computeFeatures.basic", "computeFeatures.moment", "computeFeatures.haralick"),
xname="x", refnames, properties=FALSE, expandRef=standardExpandRef, ...)
computeFeatures.basic(x, ref, properties=FALSE, basic.quantiles=c(0.01, 0.05, 0.5, 0.95, 0.99), xs, ...)
computeFeatures.shape(x, properties=FALSE, xs, ...)
computeFeatures.moment(x, ref, properties=FALSE, xs, ...)
computeFeatures.haralick(x, ref , properties=FALSE, haralick.nbins=32, haralick.scales=c(1, 2), xs, ...)
standardExpandRef(ref, refnames, filter = gblob())
Arguments
x
An Image object or an array containing labelled objects.
Labelled objects are pixel sets with the same unique integer value.
ref
A matrix or a list of matrices, containing the
intensity values of the reference objects.
methods.noref
A character vector containing the function names
to be called to compute features without reference intensities. Default is
computeFeatures.moment and computeFeatures.shape.
methods.ref
A character vector containing the function names
to be called to compute features with reference intensities. Default is
computeFeatures.basic, computeFeatures.moment and
computeFeatures.haralick.
xname
A character string naming the object layer. Default is
x.
refnames
A character vector naming the reference intensity
layers. Default are the names of ref, if present. If not,
reference intensity layers are named using lower-case letters.
properties
A logical. If FALSE, the default, the
function returns the feature matrix. If TRUE, the function
returns feature properties.
expandRef
A function used to expand the reference
images. Default is standardExpandRef. See Details.
basic.quantiles
A numerical vector indicating the quantiles to
compute.
haralick.nbins
An integer indicating the number of bins using
to compute the Haralick matrix. See Details.
haralick.scales
A integer vector indicating the number of
scales to use to compute the Haralick features.
xs
An optional temporary object created by
computeFeatures used for performance considerations.
filter
The filter applied to reference images using filter2 in order to add granulometry.
...
Optional arguments passed to the feature computation functions.
Details
Features are named x.y.f, where x is the object layer, y the reference
image layer and f the feature name. Examples include cell.dna.mean,
indicating mean DNA intensity computed in the cell or
nucleus.tubulin.cx, indicating the x center of mass of tubulin
computed in the nucleus region.
The function computeFeatures computes sets of
features. Features are organized in 4 sets, each computed by a
different function. The function computeFeatures.basic
computes spatial-independent statistics on pixel intensities:
b.mean: mean intensity
b.sd: standard deviation intensity
b.mad: mad intensity
b.q*: quantile intensity
The function computeFeatures.shape computes features that
quantify object shape:
s.area: area size (in pixels)
s.perimeter: perimeter (in pixels)
s.radius.mean: mean radius (in pixels)
s.radius.sd: standard deviation of the mean radius (in pixels)
s.radius.max: max radius (in pixels)
s.radius.min: min radius (in pixels)
The function computeFeatures.moment computes features
related to object image moments, which can be computed with or without
reference intensities:
m.cx: center of mass x (in pixels)
m.cy: center of mass y (in pixels)
m.majoraxis: elliptical fit major axis (in pixels)
m.eccentricity: elliptical eccentricity defined by
sqrt(1-minoraxis^2/majoraxis^2). Circle eccentricity is 0 and straight
line eccentricity is 1.
m.theta: object angle (in radians)
The function computeFeatures.haralick computes features
that quantify pixel texture. Features are named according to
Haralick's original paper.
Value
If properties if FALSE (by default), computeFeatures
returns a matrix of n cells times p features, where p depends of
the options given to the function. Returns NULL if no object is
present.
If properties if TRUE, computeFeatures
returns a matrix of p features times 2 properties (translation and
rotation invariance). Feature properties are useful to filter out
features that may not be needed for specific tasks, e.g. cell
position when doing cell classification.
Author(s)
Gregoire Pau, gregoire.pau@embl.de, 2011
References
R. M. Haralick, K Shanmugam and Its'Hak Deinstein (1979). Textural Features for Image
Classification. IEEE Transactions on Systems, Man and Cybernetics.
See Also
Examples
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## load and segment nucleus
y = readImage(system.file("images", "nuclei.tif", package="EBImage"))[,,1]
x = thresh(y, 10, 10, 0.05)
x = opening(x, makeBrush(5, shape='disc'))
x = bwlabel(x)
display(y, title="Cell nuclei")
display(x, title="Segmented nuclei")
## compute shape features
fts = computeFeatures.shape(x)
fts
## compute features
ft = computeFeatures(x, y, xname="nucleus")
cat("median features are:\n")
apply(ft, 2, median)
## compute feature properties
ftp = computeFeatures(x, y, properties=TRUE, xname="nucleus")
ftp
Example output
s.area s.perimeter s.radius.mean s.radius.sd s.radius.min s.radius.max
1 75 40 5.384756 2.5473087 1.4630875 9.598991
2 286 95 11.914279 6.2510079 1.6594562 22.733608
3 211 61 8.463546 2.8625585 3.9930738 12.369067
4 321 56 9.781896 1.6472487 6.2744674 12.269780
5 502 80 13.182665 4.1268371 6.3981687 19.601315
6 423 70 11.193220 2.0760003 5.6671268 14.562252
7 379 62 10.640572 1.6783868 7.8950748 13.529297
8 330 61 9.992652 1.7385299 6.7247892 13.441793
9 488 81 12.307053 3.3772075 6.2079250 18.124605
10 204 60 7.874377 2.8414135 2.3777908 12.207398
11 44 19 3.332189 0.4755575 2.3139945 4.095806
12 311 67 9.494065 3.0864776 1.5623237 13.654335
13 44 19 3.305533 0.3703584 2.5004155 3.864749
14 420 67 11.123299 1.2934341 8.6474474 13.257580
15 389 62 10.703034 1.1018437 8.0865505 12.705296
16 621 87 13.992169 2.7306336 8.2129473 18.503919
17 361 75 10.111333 3.3552681 2.9636314 14.539479
18 357 64 10.244403 1.8122203 7.0146679 13.037899
19 435 69 11.305686 1.1548827 8.8329856 13.834683
20 129 36 5.980610 0.9313067 4.1970191 7.498405
21 298 58 9.361134 2.0215001 4.6039648 12.788327
22 193 55 8.004665 2.7831936 3.3462450 13.494008
23 518 77 12.850968 1.7065512 9.7696871 16.372055
24 375 66 10.605399 1.6752607 6.0521153 13.707692
25 296 60 9.568764 2.7346801 4.1162618 13.240479
26 293 59 9.326125 2.1519705 4.5920944 12.679326
27 319 59 9.592548 1.5283310 5.2950031 11.936404
28 298 53 9.330598 0.8379296 7.9462864 11.174941
29 41 24 3.425799 1.3888233 1.3076962 5.631169
30 420 71 11.239198 2.0212645 7.1682393 15.389424
31 426 71 11.499226 3.2205048 4.3185267 16.412005
32 527 78 12.593632 2.7746344 7.2046491 17.092787
33 320 65 9.968671 3.3952696 3.6402744 14.971436
34 394 63 10.875879 1.6449716 7.5135722 13.660037
35 207 46 8.142217 2.1090645 4.7037973 11.353780
36 225 49 8.116555 1.8312625 4.9458964 11.162650
37 397 60 10.974379 1.5693077 7.5465408 13.719218
38 136 36 6.157999 0.7461044 4.4466141 7.640909
39 348 65 10.110098 2.8345070 3.4814810 13.567975
40 281 54 9.075496 1.5849007 6.3138101 11.906011
41 376 70 11.071847 2.7499368 6.8124286 16.161967
42 75 26 4.486989 0.7050572 2.7846791 5.607740
43 429 72 11.359828 2.5598612 5.2518552 15.312442
44 436 74 11.583097 3.0002508 4.9133656 16.382442
45 111 56 7.362079 3.6954862 1.5642082 13.581117
46 464 70 11.963935 2.3913054 6.9746626 15.853442
47 485 76 12.036427 2.2339630 7.8179711 15.559382
48 315 60 9.620033 1.9466415 5.0364229 12.744890
49 320 56 9.732844 1.2712755 7.3639012 11.877886
50 368 70 10.636651 2.4402276 5.2173963 14.980695
51 390 79 11.033786 3.5889820 1.6093382 15.952305
52 390 93 10.405770 4.0866145 1.3026739 16.318674
53 319 64 9.871016 2.7185802 5.0637055 14.532846
54 339 59 9.941373 0.9332251 8.2734958 11.655066
55 536 77 12.687949 2.3561859 8.2420786 16.448169
56 342 66 10.049837 2.9300224 2.8931460 14.155221
57 507 81 12.527034 3.2253364 6.2175786 17.870011
58 248 53 8.552597 1.7548511 4.2934790 11.441401
59 345 69 10.565709 3.4667560 3.1461295 15.804499
60 351 65 10.169064 2.1134302 5.2726154 13.820292
61 421 73 11.224041 3.0790975 3.9368729 16.263845
62 358 60 10.230394 0.7600282 8.7451733 11.632342
63 364 63 10.597760 2.2577422 7.1604897 15.149611
64 207 49 7.727419 1.1778694 5.2080817 10.220110
65 380 82 11.863925 5.1505547 2.0893558 19.863548
66 582 85 13.019464 2.5345198 7.0551853 16.635515
67 309 58 9.500583 1.4418692 6.3927166 11.827988
68 408 87 11.064216 4.1956813 0.5892416 16.864643
69 273 54 8.889901 1.4330635 5.7806557 11.055804
70 315 75 8.611755 3.1603344 0.5259489 12.309750
71 352 82 10.428098 4.4000913 2.2639941 17.451083
72 400 66 11.139322 2.3482859 7.3767342 15.324505
73 262 53 8.669239 0.9545777 6.9192824 10.276785
74 345 68 10.415186 3.3805793 3.2596012 15.656468
75 321 74 10.503623 3.7010085 4.3515402 17.611904
76 16 12 1.833022 0.6018740 0.9718253 2.635231
median features are:
nucleus.0.m.cx nucleus.0.m.cy nucleus.0.m.majoraxis
2.760080e+02 2.917190e+02 2.716022e+01
nucleus.0.m.eccentricity nucleus.0.m.theta nucleus.0.s.area
7.799645e-01 6.983438e-02 3.450000e+02
nucleus.0.s.perimeter nucleus.0.s.radius.mean nucleus.0.s.radius.sd
6.450000e+01 1.019973e+01 2.245853e+00
nucleus.0.s.radius.min nucleus.0.s.radius.max nucleus.a.b.mean
5.135894e+00 1.365719e+01 5.537696e-01
nucleus.a.b.sd nucleus.a.b.mad nucleus.a.b.q001
1.184311e-01 1.162824e-01 3.151373e-01
nucleus.a.b.q005 nucleus.a.b.q05 nucleus.a.b.q095
3.598039e-01 5.647059e-01 7.411765e-01
nucleus.a.b.q099 nucleus.a.m.cx nucleus.a.m.cy
7.681569e-01 2.759344e+02 2.918791e+02
nucleus.a.m.majoraxis nucleus.a.m.eccentricity nucleus.a.m.theta
2.563950e+01 7.673224e-01 2.233263e-02
nucleus.a.h.asm.s1 nucleus.a.h.con.s1 nucleus.a.h.cor.s1
2.238844e-02 3.645172e+00 8.512804e-01
nucleus.a.h.var.s1 nucleus.a.h.idm.s1 nucleus.a.h.sav.s1
1.240606e+01 5.039755e-01 3.630086e+01
nucleus.a.h.sva.s1 nucleus.a.h.sen.s1 nucleus.a.h.ent.s1
1.269986e+03 1.339942e+00 1.816435e+00
nucleus.a.h.dva.s1 nucleus.a.h.den.s1 nucleus.a.h.f12.s1
3.645172e+00 6.324399e-01 2.786244e-01
nucleus.a.h.f13.s1 nucleus.a.h.asm.s2 nucleus.a.h.con.s2
6.659335e-01 1.982790e-02 9.450356e+00
nucleus.a.h.cor.s2 nucleus.a.h.var.s2 nucleus.a.h.idm.s2
6.010386e-01 1.226194e+01 3.643872e-01
nucleus.a.h.sav.s2 nucleus.a.h.sva.s2 nucleus.a.h.sen.s2
3.686993e+01 1.302210e+03 1.294284e+00
nucleus.a.h.ent.s2 nucleus.a.h.dva.s2 nucleus.a.h.den.s2
1.858567e+00 9.450356e+00 8.014289e-01
nucleus.a.h.f12.s2 nucleus.a.h.f13.s2 nucleus.Ba.b.mean
1.731739e-01 5.477548e-01 6.112350e-01
nucleus.Ba.b.sd nucleus.Ba.b.mad nucleus.Ba.b.q001
2.347311e-01 2.489820e-01 1.576757e-01
nucleus.Ba.b.q005 nucleus.Ba.b.q05 nucleus.Ba.b.q095
2.603433e-01 6.334505e-01 1.033540e+00
nucleus.Ba.b.q099 nucleus.Ba.m.cx nucleus.Ba.m.cy
1.132751e+00 2.759874e+02 2.918643e+02
nucleus.Ba.m.majoraxis nucleus.Ba.m.eccentricity nucleus.Ba.m.theta
2.727524e+01 7.903687e-01 8.621972e-03
nucleus.Ba.h.asm.s1 nucleus.Ba.h.con.s1 nucleus.Ba.h.cor.s1
1.065775e-02 2.245891e+01 7.043244e-01
nucleus.Ba.h.var.s1 nucleus.Ba.h.idm.s1 nucleus.Ba.h.sav.s1
4.250613e+01 3.103933e-01 4.025579e+01
nucleus.Ba.h.sva.s1 nucleus.Ba.h.sen.s1 nucleus.Ba.h.ent.s1
1.637727e+03 1.568549e+00 2.330354e+00
nucleus.Ba.h.dva.s1 nucleus.Ba.h.den.s1 nucleus.Ba.h.f12.s1
2.245891e+01 9.647075e-01 1.800243e-01
nucleus.Ba.h.f13.s1 nucleus.Ba.h.asm.s2 nucleus.Ba.h.con.s2
5.919088e-01 9.993056e-03 5.253647e+01
nucleus.Ba.h.cor.s2 nucleus.Ba.h.var.s2 nucleus.Ba.h.idm.s2
3.220357e-01 4.363279e+01 2.085173e-01
nucleus.Ba.h.sav.s2 nucleus.Ba.h.sva.s2 nucleus.Ba.h.sen.s2
4.089912e+01 1.646988e+03 1.489651e+00
nucleus.Ba.h.ent.s2 nucleus.Ba.h.dva.s2 nucleus.Ba.h.den.s2
2.186038e+00 5.253647e+01 1.126337e+00
nucleus.Ba.h.f12.s2 nucleus.Ba.h.f13.s2
1.735806e-01 5.638763e-01
name translation.invariant rotation.invariant
1 nucleus.0.m.cx FALSE TRUE
2 nucleus.0.m.cy FALSE TRUE
3 nucleus.0.m.majoraxis TRUE TRUE
4 nucleus.0.m.eccentricity TRUE TRUE
5 nucleus.0.m.theta TRUE FALSE
6 nucleus.0.s.area TRUE TRUE
7 nucleus.0.s.perimeter TRUE TRUE
8 nucleus.0.s.radius.mean TRUE TRUE
9 nucleus.0.s.radius.sd TRUE TRUE
10 nucleus.0.s.radius.min TRUE TRUE
11 nucleus.0.s.radius.max TRUE TRUE
12 nucleus.a.b.mean TRUE TRUE
13 nucleus.a.b.sd TRUE TRUE
14 nucleus.a.b.mad TRUE TRUE
15 nucleus.a.b.q001 TRUE TRUE
16 nucleus.a.b.q005 TRUE TRUE
17 nucleus.a.b.q05 TRUE TRUE
18 nucleus.a.b.q095 TRUE TRUE
19 nucleus.a.b.q099 TRUE TRUE
20 nucleus.a.m.cx FALSE TRUE
21 nucleus.a.m.cy FALSE TRUE
22 nucleus.a.m.majoraxis TRUE TRUE
23 nucleus.a.m.eccentricity TRUE TRUE
24 nucleus.a.m.theta TRUE FALSE
25 nucleus.a.h.asm.s1 TRUE TRUE
26 nucleus.a.h.con.s1 TRUE TRUE
27 nucleus.a.h.cor.s1 TRUE TRUE
28 nucleus.a.h.var.s1 TRUE TRUE
29 nucleus.a.h.idm.s1 TRUE TRUE
30 nucleus.a.h.sav.s1 TRUE TRUE
31 nucleus.a.h.sva.s1 TRUE TRUE
32 nucleus.a.h.sen.s1 TRUE TRUE
33 nucleus.a.h.ent.s1 TRUE TRUE
34 nucleus.a.h.dva.s1 TRUE TRUE
35 nucleus.a.h.den.s1 TRUE TRUE
36 nucleus.a.h.f12.s1 TRUE TRUE
37 nucleus.a.h.f13.s1 TRUE TRUE
38 nucleus.a.h.asm.s2 TRUE TRUE
39 nucleus.a.h.con.s2 TRUE TRUE
40 nucleus.a.h.cor.s2 TRUE TRUE
41 nucleus.a.h.var.s2 TRUE TRUE
42 nucleus.a.h.idm.s2 TRUE TRUE
43 nucleus.a.h.sav.s2 TRUE TRUE
44 nucleus.a.h.sva.s2 TRUE TRUE
45 nucleus.a.h.sen.s2 TRUE TRUE
46 nucleus.a.h.ent.s2 TRUE TRUE
47 nucleus.a.h.dva.s2 TRUE TRUE
48 nucleus.a.h.den.s2 TRUE TRUE
49 nucleus.a.h.f12.s2 TRUE TRUE
50 nucleus.a.h.f13.s2 TRUE TRUE
51 nucleus.Ba.b.mean TRUE TRUE
52 nucleus.Ba.b.sd TRUE TRUE
53 nucleus.Ba.b.mad TRUE TRUE
54 nucleus.Ba.b.q001 TRUE TRUE
55 nucleus.Ba.b.q005 TRUE TRUE
56 nucleus.Ba.b.q05 TRUE TRUE
57 nucleus.Ba.b.q095 TRUE TRUE
58 nucleus.Ba.b.q099 TRUE TRUE
59 nucleus.Ba.m.cx FALSE TRUE
60 nucleus.Ba.m.cy FALSE TRUE
61 nucleus.Ba.m.majoraxis TRUE TRUE
62 nucleus.Ba.m.eccentricity TRUE TRUE
63 nucleus.Ba.m.theta TRUE FALSE
64 nucleus.Ba.h.asm.s1 TRUE TRUE
65 nucleus.Ba.h.con.s1 TRUE TRUE
66 nucleus.Ba.h.cor.s1 TRUE TRUE
67 nucleus.Ba.h.var.s1 TRUE TRUE
68 nucleus.Ba.h.idm.s1 TRUE TRUE
69 nucleus.Ba.h.sav.s1 TRUE TRUE
70 nucleus.Ba.h.sva.s1 TRUE TRUE
71 nucleus.Ba.h.sen.s1 TRUE TRUE
72 nucleus.Ba.h.ent.s1 TRUE TRUE
73 nucleus.Ba.h.dva.s1 TRUE TRUE
74 nucleus.Ba.h.den.s1 TRUE TRUE
75 nucleus.Ba.h.f12.s1 TRUE TRUE
76 nucleus.Ba.h.f13.s1 TRUE TRUE
77 nucleus.Ba.h.asm.s2 TRUE TRUE
78 nucleus.Ba.h.con.s2 TRUE TRUE
79 nucleus.Ba.h.cor.s2 TRUE TRUE
80 nucleus.Ba.h.var.s2 TRUE TRUE
81 nucleus.Ba.h.idm.s2 TRUE TRUE
82 nucleus.Ba.h.sav.s2 TRUE TRUE
83 nucleus.Ba.h.sva.s2 TRUE TRUE
84 nucleus.Ba.h.sen.s2 TRUE TRUE
85 nucleus.Ba.h.ent.s2 TRUE TRUE
86 nucleus.Ba.h.dva.s2 TRUE TRUE
87 nucleus.Ba.h.den.s2 TRUE TRUE
88 nucleus.Ba.h.f12.s2 TRUE TRUE
89 nucleus.Ba.h.f13.s2 TRUE TRUE
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Description Usage Arguments Details Value Author(s) References See Also Examples
View source: R/computeFeatures.R
Description
Computes morphological and texture features from image objects.
Usage
1 2 3 4 5 6 7 8 9 10 | computeFeatures(x, ref, methods.noref=c("computeFeatures.moment", "computeFeatures.shape"),
methods.ref=c("computeFeatures.basic", "computeFeatures.moment", "computeFeatures.haralick"),
xname="x", refnames, properties=FALSE, expandRef=standardExpandRef, ...)
computeFeatures.basic(x, ref, properties=FALSE, basic.quantiles=c(0.01, 0.05, 0.5, 0.95, 0.99), xs, ...)
computeFeatures.shape(x, properties=FALSE, xs, ...)
computeFeatures.moment(x, ref, properties=FALSE, xs, ...)
computeFeatures.haralick(x, ref , properties=FALSE, haralick.nbins=32, haralick.scales=c(1, 2), xs, ...)
standardExpandRef(ref, refnames, filter = gblob())
|
Arguments
x |
An |
ref |
A matrix or a list of matrices, containing the intensity values of the reference objects. |
methods.noref |
A character vector containing the function names
to be called to compute features without reference intensities. Default is
|
methods.ref |
A character vector containing the function names
to be called to compute features with reference intensities. Default is
|
xname |
A character string naming the object layer. Default is
|
refnames |
A character vector naming the reference intensity
layers. Default are the names of |
properties |
A logical. If |
expandRef |
A function used to expand the reference
images. Default is |
basic.quantiles |
A numerical vector indicating the quantiles to compute. |
haralick.nbins |
An integer indicating the number of bins using to compute the Haralick matrix. See Details. |
haralick.scales |
A integer vector indicating the number of scales to use to compute the Haralick features. |
xs |
An optional temporary object created by
|
filter |
The filter applied to reference images using |
... |
Optional arguments passed to the feature computation functions. |
Details
Features are named x.y.f, where x is the object layer, y the reference
image layer and f the feature name. Examples include cell.dna.mean,
indicating mean DNA intensity computed in the cell or
nucleus.tubulin.cx, indicating the x center of mass of tubulin
computed in the nucleus region.
The function computeFeatures computes sets of
features. Features are organized in 4 sets, each computed by a
different function. The function computeFeatures.basic
computes spatial-independent statistics on pixel intensities:
b.mean: mean intensity
b.sd: standard deviation intensity
b.mad: mad intensity
b.q*: quantile intensity
The function computeFeatures.shape computes features that
quantify object shape:
s.area: area size (in pixels)
s.perimeter: perimeter (in pixels)
s.radius.mean: mean radius (in pixels)
s.radius.sd: standard deviation of the mean radius (in pixels)
s.radius.max: max radius (in pixels)
s.radius.min: min radius (in pixels)
The function computeFeatures.moment computes features
related to object image moments, which can be computed with or without
reference intensities:
m.cx: center of mass x (in pixels)
m.cy: center of mass y (in pixels)
m.majoraxis: elliptical fit major axis (in pixels)
m.eccentricity: elliptical eccentricity defined by sqrt(1-minoraxis^2/majoraxis^2). Circle eccentricity is 0 and straight line eccentricity is 1.
m.theta: object angle (in radians)
The function computeFeatures.haralick computes features
that quantify pixel texture. Features are named according to
Haralick's original paper.
Value
If properties if FALSE (by default), computeFeatures
returns a matrix of n cells times p features, where p depends of
the options given to the function. Returns NULL if no object is
present.
If properties if TRUE, computeFeatures
returns a matrix of p features times 2 properties (translation and
rotation invariance). Feature properties are useful to filter out
features that may not be needed for specific tasks, e.g. cell
position when doing cell classification.
Author(s)
Gregoire Pau, gregoire.pau@embl.de, 2011
References
R. M. Haralick, K Shanmugam and Its'Hak Deinstein (1979). Textural Features for Image Classification. IEEE Transactions on Systems, Man and Cybernetics.
See Also
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | ## load and segment nucleus
y = readImage(system.file("images", "nuclei.tif", package="EBImage"))[,,1]
x = thresh(y, 10, 10, 0.05)
x = opening(x, makeBrush(5, shape='disc'))
x = bwlabel(x)
display(y, title="Cell nuclei")
display(x, title="Segmented nuclei")
## compute shape features
fts = computeFeatures.shape(x)
fts
## compute features
ft = computeFeatures(x, y, xname="nucleus")
cat("median features are:\n")
apply(ft, 2, median)
## compute feature properties
ftp = computeFeatures(x, y, properties=TRUE, xname="nucleus")
ftp
|
Example output
s.area s.perimeter s.radius.mean s.radius.sd s.radius.min s.radius.max
1 75 40 5.384756 2.5473087 1.4630875 9.598991
2 286 95 11.914279 6.2510079 1.6594562 22.733608
3 211 61 8.463546 2.8625585 3.9930738 12.369067
4 321 56 9.781896 1.6472487 6.2744674 12.269780
5 502 80 13.182665 4.1268371 6.3981687 19.601315
6 423 70 11.193220 2.0760003 5.6671268 14.562252
7 379 62 10.640572 1.6783868 7.8950748 13.529297
8 330 61 9.992652 1.7385299 6.7247892 13.441793
9 488 81 12.307053 3.3772075 6.2079250 18.124605
10 204 60 7.874377 2.8414135 2.3777908 12.207398
11 44 19 3.332189 0.4755575 2.3139945 4.095806
12 311 67 9.494065 3.0864776 1.5623237 13.654335
13 44 19 3.305533 0.3703584 2.5004155 3.864749
14 420 67 11.123299 1.2934341 8.6474474 13.257580
15 389 62 10.703034 1.1018437 8.0865505 12.705296
16 621 87 13.992169 2.7306336 8.2129473 18.503919
17 361 75 10.111333 3.3552681 2.9636314 14.539479
18 357 64 10.244403 1.8122203 7.0146679 13.037899
19 435 69 11.305686 1.1548827 8.8329856 13.834683
20 129 36 5.980610 0.9313067 4.1970191 7.498405
21 298 58 9.361134 2.0215001 4.6039648 12.788327
22 193 55 8.004665 2.7831936 3.3462450 13.494008
23 518 77 12.850968 1.7065512 9.7696871 16.372055
24 375 66 10.605399 1.6752607 6.0521153 13.707692
25 296 60 9.568764 2.7346801 4.1162618 13.240479
26 293 59 9.326125 2.1519705 4.5920944 12.679326
27 319 59 9.592548 1.5283310 5.2950031 11.936404
28 298 53 9.330598 0.8379296 7.9462864 11.174941
29 41 24 3.425799 1.3888233 1.3076962 5.631169
30 420 71 11.239198 2.0212645 7.1682393 15.389424
31 426 71 11.499226 3.2205048 4.3185267 16.412005
32 527 78 12.593632 2.7746344 7.2046491 17.092787
33 320 65 9.968671 3.3952696 3.6402744 14.971436
34 394 63 10.875879 1.6449716 7.5135722 13.660037
35 207 46 8.142217 2.1090645 4.7037973 11.353780
36 225 49 8.116555 1.8312625 4.9458964 11.162650
37 397 60 10.974379 1.5693077 7.5465408 13.719218
38 136 36 6.157999 0.7461044 4.4466141 7.640909
39 348 65 10.110098 2.8345070 3.4814810 13.567975
40 281 54 9.075496 1.5849007 6.3138101 11.906011
41 376 70 11.071847 2.7499368 6.8124286 16.161967
42 75 26 4.486989 0.7050572 2.7846791 5.607740
43 429 72 11.359828 2.5598612 5.2518552 15.312442
44 436 74 11.583097 3.0002508 4.9133656 16.382442
45 111 56 7.362079 3.6954862 1.5642082 13.581117
46 464 70 11.963935 2.3913054 6.9746626 15.853442
47 485 76 12.036427 2.2339630 7.8179711 15.559382
48 315 60 9.620033 1.9466415 5.0364229 12.744890
49 320 56 9.732844 1.2712755 7.3639012 11.877886
50 368 70 10.636651 2.4402276 5.2173963 14.980695
51 390 79 11.033786 3.5889820 1.6093382 15.952305
52 390 93 10.405770 4.0866145 1.3026739 16.318674
53 319 64 9.871016 2.7185802 5.0637055 14.532846
54 339 59 9.941373 0.9332251 8.2734958 11.655066
55 536 77 12.687949 2.3561859 8.2420786 16.448169
56 342 66 10.049837 2.9300224 2.8931460 14.155221
57 507 81 12.527034 3.2253364 6.2175786 17.870011
58 248 53 8.552597 1.7548511 4.2934790 11.441401
59 345 69 10.565709 3.4667560 3.1461295 15.804499
60 351 65 10.169064 2.1134302 5.2726154 13.820292
61 421 73 11.224041 3.0790975 3.9368729 16.263845
62 358 60 10.230394 0.7600282 8.7451733 11.632342
63 364 63 10.597760 2.2577422 7.1604897 15.149611
64 207 49 7.727419 1.1778694 5.2080817 10.220110
65 380 82 11.863925 5.1505547 2.0893558 19.863548
66 582 85 13.019464 2.5345198 7.0551853 16.635515
67 309 58 9.500583 1.4418692 6.3927166 11.827988
68 408 87 11.064216 4.1956813 0.5892416 16.864643
69 273 54 8.889901 1.4330635 5.7806557 11.055804
70 315 75 8.611755 3.1603344 0.5259489 12.309750
71 352 82 10.428098 4.4000913 2.2639941 17.451083
72 400 66 11.139322 2.3482859 7.3767342 15.324505
73 262 53 8.669239 0.9545777 6.9192824 10.276785
74 345 68 10.415186 3.3805793 3.2596012 15.656468
75 321 74 10.503623 3.7010085 4.3515402 17.611904
76 16 12 1.833022 0.6018740 0.9718253 2.635231
median features are:
nucleus.0.m.cx nucleus.0.m.cy nucleus.0.m.majoraxis
2.760080e+02 2.917190e+02 2.716022e+01
nucleus.0.m.eccentricity nucleus.0.m.theta nucleus.0.s.area
7.799645e-01 6.983438e-02 3.450000e+02
nucleus.0.s.perimeter nucleus.0.s.radius.mean nucleus.0.s.radius.sd
6.450000e+01 1.019973e+01 2.245853e+00
nucleus.0.s.radius.min nucleus.0.s.radius.max nucleus.a.b.mean
5.135894e+00 1.365719e+01 5.537696e-01
nucleus.a.b.sd nucleus.a.b.mad nucleus.a.b.q001
1.184311e-01 1.162824e-01 3.151373e-01
nucleus.a.b.q005 nucleus.a.b.q05 nucleus.a.b.q095
3.598039e-01 5.647059e-01 7.411765e-01
nucleus.a.b.q099 nucleus.a.m.cx nucleus.a.m.cy
7.681569e-01 2.759344e+02 2.918791e+02
nucleus.a.m.majoraxis nucleus.a.m.eccentricity nucleus.a.m.theta
2.563950e+01 7.673224e-01 2.233263e-02
nucleus.a.h.asm.s1 nucleus.a.h.con.s1 nucleus.a.h.cor.s1
2.238844e-02 3.645172e+00 8.512804e-01
nucleus.a.h.var.s1 nucleus.a.h.idm.s1 nucleus.a.h.sav.s1
1.240606e+01 5.039755e-01 3.630086e+01
nucleus.a.h.sva.s1 nucleus.a.h.sen.s1 nucleus.a.h.ent.s1
1.269986e+03 1.339942e+00 1.816435e+00
nucleus.a.h.dva.s1 nucleus.a.h.den.s1 nucleus.a.h.f12.s1
3.645172e+00 6.324399e-01 2.786244e-01
nucleus.a.h.f13.s1 nucleus.a.h.asm.s2 nucleus.a.h.con.s2
6.659335e-01 1.982790e-02 9.450356e+00
nucleus.a.h.cor.s2 nucleus.a.h.var.s2 nucleus.a.h.idm.s2
6.010386e-01 1.226194e+01 3.643872e-01
nucleus.a.h.sav.s2 nucleus.a.h.sva.s2 nucleus.a.h.sen.s2
3.686993e+01 1.302210e+03 1.294284e+00
nucleus.a.h.ent.s2 nucleus.a.h.dva.s2 nucleus.a.h.den.s2
1.858567e+00 9.450356e+00 8.014289e-01
nucleus.a.h.f12.s2 nucleus.a.h.f13.s2 nucleus.Ba.b.mean
1.731739e-01 5.477548e-01 6.112350e-01
nucleus.Ba.b.sd nucleus.Ba.b.mad nucleus.Ba.b.q001
2.347311e-01 2.489820e-01 1.576757e-01
nucleus.Ba.b.q005 nucleus.Ba.b.q05 nucleus.Ba.b.q095
2.603433e-01 6.334505e-01 1.033540e+00
nucleus.Ba.b.q099 nucleus.Ba.m.cx nucleus.Ba.m.cy
1.132751e+00 2.759874e+02 2.918643e+02
nucleus.Ba.m.majoraxis nucleus.Ba.m.eccentricity nucleus.Ba.m.theta
2.727524e+01 7.903687e-01 8.621972e-03
nucleus.Ba.h.asm.s1 nucleus.Ba.h.con.s1 nucleus.Ba.h.cor.s1
1.065775e-02 2.245891e+01 7.043244e-01
nucleus.Ba.h.var.s1 nucleus.Ba.h.idm.s1 nucleus.Ba.h.sav.s1
4.250613e+01 3.103933e-01 4.025579e+01
nucleus.Ba.h.sva.s1 nucleus.Ba.h.sen.s1 nucleus.Ba.h.ent.s1
1.637727e+03 1.568549e+00 2.330354e+00
nucleus.Ba.h.dva.s1 nucleus.Ba.h.den.s1 nucleus.Ba.h.f12.s1
2.245891e+01 9.647075e-01 1.800243e-01
nucleus.Ba.h.f13.s1 nucleus.Ba.h.asm.s2 nucleus.Ba.h.con.s2
5.919088e-01 9.993056e-03 5.253647e+01
nucleus.Ba.h.cor.s2 nucleus.Ba.h.var.s2 nucleus.Ba.h.idm.s2
3.220357e-01 4.363279e+01 2.085173e-01
nucleus.Ba.h.sav.s2 nucleus.Ba.h.sva.s2 nucleus.Ba.h.sen.s2
4.089912e+01 1.646988e+03 1.489651e+00
nucleus.Ba.h.ent.s2 nucleus.Ba.h.dva.s2 nucleus.Ba.h.den.s2
2.186038e+00 5.253647e+01 1.126337e+00
nucleus.Ba.h.f12.s2 nucleus.Ba.h.f13.s2
1.735806e-01 5.638763e-01
name translation.invariant rotation.invariant
1 nucleus.0.m.cx FALSE TRUE
2 nucleus.0.m.cy FALSE TRUE
3 nucleus.0.m.majoraxis TRUE TRUE
4 nucleus.0.m.eccentricity TRUE TRUE
5 nucleus.0.m.theta TRUE FALSE
6 nucleus.0.s.area TRUE TRUE
7 nucleus.0.s.perimeter TRUE TRUE
8 nucleus.0.s.radius.mean TRUE TRUE
9 nucleus.0.s.radius.sd TRUE TRUE
10 nucleus.0.s.radius.min TRUE TRUE
11 nucleus.0.s.radius.max TRUE TRUE
12 nucleus.a.b.mean TRUE TRUE
13 nucleus.a.b.sd TRUE TRUE
14 nucleus.a.b.mad TRUE TRUE
15 nucleus.a.b.q001 TRUE TRUE
16 nucleus.a.b.q005 TRUE TRUE
17 nucleus.a.b.q05 TRUE TRUE
18 nucleus.a.b.q095 TRUE TRUE
19 nucleus.a.b.q099 TRUE TRUE
20 nucleus.a.m.cx FALSE TRUE
21 nucleus.a.m.cy FALSE TRUE
22 nucleus.a.m.majoraxis TRUE TRUE
23 nucleus.a.m.eccentricity TRUE TRUE
24 nucleus.a.m.theta TRUE FALSE
25 nucleus.a.h.asm.s1 TRUE TRUE
26 nucleus.a.h.con.s1 TRUE TRUE
27 nucleus.a.h.cor.s1 TRUE TRUE
28 nucleus.a.h.var.s1 TRUE TRUE
29 nucleus.a.h.idm.s1 TRUE TRUE
30 nucleus.a.h.sav.s1 TRUE TRUE
31 nucleus.a.h.sva.s1 TRUE TRUE
32 nucleus.a.h.sen.s1 TRUE TRUE
33 nucleus.a.h.ent.s1 TRUE TRUE
34 nucleus.a.h.dva.s1 TRUE TRUE
35 nucleus.a.h.den.s1 TRUE TRUE
36 nucleus.a.h.f12.s1 TRUE TRUE
37 nucleus.a.h.f13.s1 TRUE TRUE
38 nucleus.a.h.asm.s2 TRUE TRUE
39 nucleus.a.h.con.s2 TRUE TRUE
40 nucleus.a.h.cor.s2 TRUE TRUE
41 nucleus.a.h.var.s2 TRUE TRUE
42 nucleus.a.h.idm.s2 TRUE TRUE
43 nucleus.a.h.sav.s2 TRUE TRUE
44 nucleus.a.h.sva.s2 TRUE TRUE
45 nucleus.a.h.sen.s2 TRUE TRUE
46 nucleus.a.h.ent.s2 TRUE TRUE
47 nucleus.a.h.dva.s2 TRUE TRUE
48 nucleus.a.h.den.s2 TRUE TRUE
49 nucleus.a.h.f12.s2 TRUE TRUE
50 nucleus.a.h.f13.s2 TRUE TRUE
51 nucleus.Ba.b.mean TRUE TRUE
52 nucleus.Ba.b.sd TRUE TRUE
53 nucleus.Ba.b.mad TRUE TRUE
54 nucleus.Ba.b.q001 TRUE TRUE
55 nucleus.Ba.b.q005 TRUE TRUE
56 nucleus.Ba.b.q05 TRUE TRUE
57 nucleus.Ba.b.q095 TRUE TRUE
58 nucleus.Ba.b.q099 TRUE TRUE
59 nucleus.Ba.m.cx FALSE TRUE
60 nucleus.Ba.m.cy FALSE TRUE
61 nucleus.Ba.m.majoraxis TRUE TRUE
62 nucleus.Ba.m.eccentricity TRUE TRUE
63 nucleus.Ba.m.theta TRUE FALSE
64 nucleus.Ba.h.asm.s1 TRUE TRUE
65 nucleus.Ba.h.con.s1 TRUE TRUE
66 nucleus.Ba.h.cor.s1 TRUE TRUE
67 nucleus.Ba.h.var.s1 TRUE TRUE
68 nucleus.Ba.h.idm.s1 TRUE TRUE
69 nucleus.Ba.h.sav.s1 TRUE TRUE
70 nucleus.Ba.h.sva.s1 TRUE TRUE
71 nucleus.Ba.h.sen.s1 TRUE TRUE
72 nucleus.Ba.h.ent.s1 TRUE TRUE
73 nucleus.Ba.h.dva.s1 TRUE TRUE
74 nucleus.Ba.h.den.s1 TRUE TRUE
75 nucleus.Ba.h.f12.s1 TRUE TRUE
76 nucleus.Ba.h.f13.s1 TRUE TRUE
77 nucleus.Ba.h.asm.s2 TRUE TRUE
78 nucleus.Ba.h.con.s2 TRUE TRUE
79 nucleus.Ba.h.cor.s2 TRUE TRUE
80 nucleus.Ba.h.var.s2 TRUE TRUE
81 nucleus.Ba.h.idm.s2 TRUE TRUE
82 nucleus.Ba.h.sav.s2 TRUE TRUE
83 nucleus.Ba.h.sva.s2 TRUE TRUE
84 nucleus.Ba.h.sen.s2 TRUE TRUE
85 nucleus.Ba.h.ent.s2 TRUE TRUE
86 nucleus.Ba.h.dva.s2 TRUE TRUE
87 nucleus.Ba.h.den.s2 TRUE TRUE
88 nucleus.Ba.h.f12.s2 TRUE TRUE
89 nucleus.Ba.h.f13.s2 TRUE TRUE
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