efg’s R Notes: EBImage: Moment Features
Basic | Haralick | Moment | Shape
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 [pixels]
- m.cy: center of mass y [pixels]
- m.majoraxis: elliptical fit major axis [pixels]
- m.eccentricity: elliptical eccentricity defined by \(\sqrt{1 - \frac {MinorAxis^2}{MajorAxis^2}}\). Circle eccentricity is 0 and straight line eccentricity is 1.
- m.theta: object angle [radians]
All moment features have a prefix “m.”.
library(EBImage)computeFeatures.moment(x, ref, properties=FALSE, xs, ...)List properties of moment features
moment.properties <- computeFeatures.moment(properties=TRUE)
moment.properties name translation.invariant rotation.invariant
1 m.cx FALSE TRUE
2 m.cy FALSE TRUE
3 m.majoraxis TRUE TRUE
4 m.eccentricity TRUE TRUE
5 m.theta TRUE FALSELoad and segment nucleus
par(mfrow=c(1,2))
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 moment features
momentFeatures <- computeFeatures.moment(x, y)
str(momentFeatures) num [1:76, 1:5] 121.9 209.5 498 15.6 355.2 ...
- attr(*, "dimnames")=List of 2
..$ : chr [1:76] "1" "2" "3" "4" ...
..$ : chr [1:5] "m.cx" "m.cy" "m.majoraxis" "m.eccentricity" ...options(digits=4)
momentFeatures m.cx m.cy m.majoraxis m.eccentricity m.theta
1 121.91 2.157 18.933 0.9724 0.014261
2 209.51 4.526 44.864 0.9686 -0.123709
3 497.96 5.021 26.230 0.9130 -0.166041
4 15.58 21.895 23.258 0.7179 0.662312
5 355.23 40.674 37.345 0.9113 -0.717877
6 201.10 50.334 26.362 0.6709 -1.154433
7 270.05 48.010 24.900 0.7202 -0.564551
8 103.05 59.029 23.259 0.7137 0.680846
9 220.77 73.953 33.362 0.8462 1.567322
10 20.26 74.290 25.234 0.8933 -1.231533
11 12.78 66.938 8.743 0.6998 0.566899
12 54.81 86.256 25.996 0.8133 -1.470879
13 239.20 89.861 8.230 0.5990 0.469316
14 428.32 106.267 25.112 0.6460 -0.030111
15 172.20 110.430 24.354 0.6024 1.200462
16 281.82 113.338 35.778 0.7672 -0.533530
17 482.92 144.828 30.164 0.8537 -0.883514
18 184.73 143.261 25.748 0.7552 0.030404
19 369.87 148.018 24.347 0.5243 1.096711
20 451.99 146.245 15.066 0.7075 1.364882
21 42.24 159.111 23.001 0.7568 1.426966
22 506.50 160.000 23.456 0.9061 1.459597
23 139.86 166.999 29.286 0.6145 -0.308636
24 75.34 167.560 25.531 0.6965 1.141134
25 440.96 176.292 26.576 0.8752 0.364926
26 57.59 198.806 23.128 0.7651 1.184429
27 456.83 204.478 22.199 0.6342 1.416205
28 486.60 206.825 19.309 0.4124 0.944504
29 508.79 203.315 11.876 0.9348 1.564039
30 379.92 225.597 25.384 0.6511 0.890749
31 328.06 237.697 31.250 0.8567 -0.525820
32 54.27 247.514 31.600 0.7939 -0.158137
33 176.79 255.942 29.427 0.9020 0.415912
34 422.01 266.012 25.451 0.7212 -0.871303
35 301.22 271.590 22.787 0.8791 -0.752424
36 483.97 275.367 20.989 0.8176 1.342576
37 79.54 291.901 25.321 0.7001 -0.576820
38 473.04 286.354 14.290 0.6340 0.463487
39 31.17 294.880 27.860 0.8405 -0.686989
40 309.90 292.537 22.653 0.7656 -0.205252
41 371.41 298.269 28.635 0.8394 0.942737
42 197.18 291.857 11.335 0.7414 -0.643245
43 243.35 300.628 29.396 0.7667 -1.413595
44 181.03 303.410 31.531 0.8277 0.152831
45 508.58 312.034 27.822 0.9838 1.565088
46 114.46 320.400 30.927 0.8084 0.973710
47 471.65 320.981 29.382 0.7673 -0.034360
48 329.83 326.653 24.555 0.7737 0.611664
49 303.95 337.434 22.384 0.6613 0.690330
50 201.87 354.075 26.968 0.7424 -0.391856
51 51.58 359.930 31.114 0.8229 -0.985669
52 144.43 362.656 33.487 0.8537 -0.429950
53 311.13 375.855 26.932 0.8553 1.323322
54 376.98 375.372 22.005 0.6021 -0.650564
55 247.96 386.266 31.341 0.7673 -1.431498
56 76.63 391.192 27.365 0.8243 -0.351000
57 109.19 403.318 33.330 0.8466 1.361160
58 494.03 394.894 20.988 0.7547 1.106236
59 424.44 399.577 30.787 0.8970 1.008747
60 215.43 412.916 24.307 0.7062 -1.512068
61 321.89 425.129 30.923 0.8439 -1.369627
62 366.18 419.180 21.840 0.4960 0.519304
63 288.52 425.301 26.334 0.7948 -1.106772
64 504.76 427.122 17.689 0.6208 1.332573
65 465.08 462.048 40.198 0.9492 0.785035
66 230.22 466.403 31.922 0.7507 -0.001315
67 140.64 471.566 21.893 0.6498 -0.156718
68 344.90 474.795 33.999 0.8344 0.385281
69 46.31 469.468 20.912 0.7006 -0.054880
70 185.78 490.943 24.141 0.7092 1.126549
71 409.80 488.483 34.496 0.8977 0.141176
72 66.14 492.366 28.173 0.8015 -0.683923
73 119.92 493.233 17.559 0.1772 -0.594441
74 282.36 496.915 30.712 0.8838 -0.597230
75 355.95 504.768 31.333 0.9026 0.221729
76 456.56 509.302 6.278 0.8778 0.007986Correlations of moment features
correlationMatrix <- cor(momentFeatures)
correlationMatrix## m.cx m.cy m.majoraxis m.eccentricity m.theta
## m.cx 1.00000 0.10868 -0.07982 0.08037 0.28069
## m.cy 0.10868 1.00000 0.06952 -0.04376 -0.07203
## m.majoraxis -0.07982 0.06952 1.00000 0.42718 -0.20672
## m.eccentricity 0.08037 -0.04376 0.42718 1.00000 -0.03487
## m.theta 0.28069 -0.07203 -0.20672 -0.03487 1.00000Heatmaps of correlation matrix
Color-coded display of correlation matrix
library(gplots) # heatmap.2
library(RColorBrewer) # brewer.palheatmap.2(correlationMatrix, dendrogram="none", Rowv=FALSE, symm=TRUE,
cellnote=format(round(correlationMatrix,2)),
main="Moment Features",
scale="none", col=brewer.pal(11,"RdBu"), margins=c(9,9), trace="none")
Dendrograms show relationships in correlation matrix
heatmap.2(correlationMatrix, key=FALSE,
cellnote=format(round(correlationMatrix,2)),
main="Moment Features",
scale="none", col=brewer.pal(11,"RdBu"), margins=c(9,9), trace="none")
A diverging palette from RColorBrewer is used for the heatmaps since correlations can range from -1 to +1. In the RdBu pallete, red is low and blue is high.
packageVersion("EBImage")## [1] '4.8.2'packageVersion("gplots")## [1] '2.16.0'packageVersion("RColorBrewer")## [1] '1.1.2'efg
2015-01-22 2326