computeFeatures: Compute object features

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:

The function computeFeatures.shape computes features that quantify object shape:

The function computeFeatures.moment computes features related to object image moments, which can be computed with or without reference intensities:

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, [email protected], 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

bwlabel, propagate

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

EBImage documentation built on Nov. 17, 2017, 12:34 p.m.