Skip to content

Commit 27abb49

Browse files
friskluftfriskluft
authored
POL5846 Online document update (3D features) PolusAI#299 
1 parent 5067845 commit 27abb49

File tree

1 file changed

+236
-2
lines changed

1 file changed

+236
-2
lines changed

‎README.md‎

Lines changed: 236 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -380,7 +380,7 @@ The output is:
380380

381381
This functionality is also available in the through the command line using the flag `--outputType`. If this flag is set to `--outputType=arrowipc` then the results will be written to an Arrow IPC file in the output directory and `--outputType=parquet` will write to a Parquet file.
382382

383-
## Available features
383+
## Available 2D features
384384
The feature extraction plugin extracts morphology and intensity based features from pairs of intensity/binary mask images and produces a csv file output. The input image should be in tiled [OME TIFF format](https://docs.openmicroscopy.org/ome-model/6.2.0/ome-tiff/specification.html). The plugin extracts the following features:
385385

386386
Nyxus provides a set of pixel intensity, morphology, texture, intensity distribution features, digital filter based features and image moments
@@ -430,7 +430,7 @@ Nyxus provides a set of pixel intensity, morphology, texture, intensity distribu
430430

431431
For the complete list of features see [Nyxus provided features](docs/source/featurelist.rst)
432432

433-
## Feature groups
433+
## 2D feature groups
434434

435435
Apart from defining your feature set by explicitly specifying comma-separated feature code, Nyxus lets a user specify popular feature groups. Supported feature groups are:
436436

@@ -451,6 +451,240 @@ Apart from defining your feature set by explicitly specifying comma-separated fe
451451
| \*wholeslide\* | Only features relevant to the whole-slides whose single ROIs match the images themselves, except shape features meaningless in the whole-slide use case and certain time-consuming texture features (GLDZM features).
452452
| \*all\* | All the features
453453

454+
## Available 3D features
455+
------------------
456+
| Nyxus feature code | Description |
457+
|--------|-------|
458+
| <b>Intensity</b> | |
459+
| 3COV | Coefficient of variation|
460+
| 3COVERED_IMAGE_INTENSITY_RANGE | Covered image intensity range |
461+
| 3ENERGY | Energy |
462+
| 3ENTROPY | Entropy |
463+
| 3EXCESS_KURTOSIS | Excess kurtosis |
464+
| 3HYPERFLATNESS | Hyperflatness |
465+
| 3HYPERSKEWNESS | Hyperskewness |
466+
| 3INTEGRATED_INTENSITY | Integrated intensity |
467+
| 3INTERQUARTILE_RANGE | Interquartile range |
468+
| 3KURTOSIS | Kurtosis |
469+
| 3MAX | Max |
470+
| 3MEAN | Mean |
471+
| 3MEAN_ABSOLUTE_DEVIATION | Mean absolute deviation |
472+
| 3MEDIAN | Median |
473+
| 3MEDIAN_ABSOLUTE_DEVIATION | Median absolute deviation |
474+
| 3MIN | Min |
475+
| 3MODE | Mode |
476+
| 3P01, 3P10, 3P25, 3P75, 3P90, 3P99 | 1%, 10%, 25%, 75%, 90%, 99% percentiles |
477+
| 3QCOD | Quantile coefficient of dispersion |
478+
| 3RANGE | Range |
479+
| 3ROBUST_MEAN | Robust mean |
480+
| 3ROBUST_MEAN_ABSOLUTE_DEVIATION | Robust mean absolute deviation |
481+
| 3ROOT_MEAN_SQUARED | Root mean squared |
482+
| 3SKEWNESS | Skewness |
483+
| 3STANDARD_DEVIATION | Standard deviation |
484+
| 3STANDARD_DEVIATION_BIASED | Biased standard deviation |
485+
| 3STANDARD_ERROR | Standard error |
486+
| 3UNIFORMITY | Uniformity |
487+
| 3UNIFORMITY_PIU | Uniformity in PIU units |
488+
| 3VARIANCE | Variance |
489+
| 3VARIANCE_BIASED | Biased variance |
490+
| <b>shape</b> | |
491+
| 3AREA | Surface area |
492+
| 3AREA_2_VOLUME | Surface area to volume ratio |
493+
| 3COMPACTNESS1 | Compactness1 |
494+
| 3COMPACTNESS2 | Compactness2 |
495+
| 3MESH_VOLUME | Mesh volume |
496+
| 3SPHERICAL_DISPROPORTION | Spherical disproportion |
497+
| 3SPHERICITY | Sphericity |
498+
| 3VOLUME_CONVEXHULL | Volume of the convex hull |
499+
| 3VOXEL_VOLUME | Volume as total of volumes of voxels |
500+
| 3MAJOR_AXIS_LEN | Major axis length |
501+
| 3MINOR_AXIS_LEN | Minor axis length |
502+
| 3LEAST_AXIS_LEN | Least axis length |
503+
| 3ELONGATION | Elongation |
504+
| 3FLATNESS | Flatness |
505+
| <b>texture</b> | |
506+
| 3GLCM_ACOR | Autocorrelation (grey level co-occurrence matrix) |
507+
| 3GLCM_ASM | Angular second moment (grey level co-occurrence matrix) |
508+
| 3GLCM_CLUPROM | Cluster prominence (grey level co-occurrence matrix) |
509+
| 3GLCM_CLUSHADE | Cluster shade (grey level co-occurrence matrix) |
510+
| 3GLCM_CLUTEND | Cluster tendency (grey level co-occurrence matrix) |
511+
| 3GLCM_CONTRAST | Contrast (grey level co-occurrence matrix) |
512+
| 3GLCM_CORRELATION | Correlation (grey level co-occurrence matrix) |
513+
| 3GLCM_DIFAVE | Defference average (grey level co-occurrence matrix) |
514+
| 3GLCM_DIFENTRO | Difference entropy (grey level co-occurrence matrix) |
515+
| 3GLCM_DIFVAR | Difference variance (grey level co-occurrence matrix) |
516+
| 3GLCM_DIS | Dissimilarity (grey level co-occurrence matrix) |
517+
| 3GLCM_ENERGY | Energy (grey level co-occurrence matrix) |
518+
| 3GLCM_ENTROPY | Entropy (grey level co-occurrence matrix) |
519+
| 3GLCM_HOM1 | Homogeneity-1 (grey level co-occurrence matrix) |
520+
| 3GLCM_HOM2 | Homogeneity-2 (grey level co-occurrence matrix) |
521+
| 3GLCM_ID | Inverse difference (grey level co-occurrence matrix) |
522+
| 3GLCM_IDN | Normalized inverse difference (grey level co-occurrence matrix) |
523+
| 3GLCM_IDM | Inverse difference moment (grey level co-occurrence matrix) |
524+
| 3GLCM_IDMN | Normalized inverse difference moment (grey level co-occurrence matrix) |
525+
| 3GLCM_INFOMEAS1 | 1st information measure of correlation (grey level co-occurrence matrix) |
526+
| 3GLCM_INFOMEAS2 | 2nd information measure of correlation (grey level co-occurrence matrix) |
527+
| 3GLCM_IV | Inverse variance (grey level co-occurrence matrix) |
528+
| 3GLCM_JAVE | Joint average (grey level co-occurrence matrix) |
529+
| 3GLCM_JE | Joint entropy (grey level co-occurrence matrix) |
530+
| 3GLCM_JMAX | Joint maximum aka "max probability" (grey level co-occurrence matrix) |
531+
| 3GLCM_JVAR | Joint variance aka "sum of squares" (grey level co-occurrence matrix) |
532+
| 3GLCM_SUMAVERAGE | Sum average (grey level co-occurrence matrix) |
533+
| 3GLCM_SUMENTROPY | Sum entropy (grey level co-occurrence matrix) |
534+
| 3GLCM_SUMVARIANCE | Sum variance (grey level co-occurrence matrix) |
535+
| 3GLCM_VARIANCE | Variance (grey level co-occurrence matrix) |
536+
| 3GLCM_ASM_AVE | directional average of 3GLCM_ASM |
537+
| 3GLCM_ACOR_AVE | directional average of 3GLCM_ACOR |
538+
| 3GLCM_CLUPROM_AVE | directional average of 3GLCM_CLUPROM |
539+
| 3GLCM_CLUSHADE_AVE | directional average of 3GLCM_CLUSHADE |
540+
| 3GLCM_CLUTEND_AVE | directional average of 3GLCM_CLUTEND |
541+
| 3GLCM_CONTRAST_AVE | directional average of 3GLCM_CONTRAST |
542+
| 3GLCM_CORRELATION_AVE | directional average of 3GLCM_CORRELATION |
543+
| 3GLCM_DIFAVE_AVE | directional average of 3GLCM_DIFAVE |
544+
| 3GLCM_DIFENTRO_AVE | directional average of 3GLCM_DIFENTRO |
545+
| 3GLCM_DIFVAR_AVE | directional average of 3GLCM_DIFVAR |
546+
| 3GLCM_DIS_AVE | directional average of 3GLCM_DIS |
547+
| 3GLCM_ENERGY_AVE | directional average of 3GLCM_ENERGY |
548+
| 3GLCM_ENTROPY_AVE | directional average of 3GLCM_ENTROPY |
549+
| 3GLCM_HOM1_AVE | directional average of 3GLCM_HOM1 |
550+
| 3GLCM_ID_AVE | directional average of 3GLCM_ID |
551+
| 3GLCM_IDN_AVE | directional average of 3GLCM_IDN |
552+
| 3GLCM_IDM_AVE | directional average of 3GLCM_IDM |
553+
| 3GLCM_IDMN_AVE | directional average of 3GLCM_IDMN |
554+
| 3GLCM_IV_AVE | directional average of 3GLCM_IV |
555+
| 3GLCM_JAVE_AVE | directional average of 3GLCM_JAVE |
556+
| 3GLCM_JE_AVE | directional average of 3GLCM_JE |
557+
| 3GLCM_INFOMEAS1_AVE | directional average of 3GLCM_INFOMEAS1 |
558+
| 3GLCM_INFOMEAS2_AVE | directional average of 3GLCM_INFOMEAS2 |
559+
| 3GLCM_VARIANCE_AVE | directional average of 3GLCM_VARIANCE |
560+
| 3GLCM_JMAX_AVE | directional average of 3GLCM_JMAX |
561+
| 3GLCM_JVAR_AVE | directional average of 3GLCM_JVAR |
562+
| 3GLCM_SUMAVERAGE_AVE | directional average of 3GLCM_SUMAVERAGE |
563+
| 3GLCM_SUMENTROPY_AVE | directional average of 3GLCM_SUMENTROPY |
564+
| 3GLCM_SUMVARIANCE_AVE | directional average of 3GLCM_SUMVARIANCE |
565+
| 3GLDM_SDE | Small dependence emphasis (grey level dependence matrix) |
566+
| 3GLDM_LDE | Large dependence emphasis (grey level dependence matrix) |
567+
| 3GLDM_GLN | Gray level non-uniformity (grey level dependence matrix) |
568+
| 3GLDM_DN | Dependence non-uniformity (grey level dependence matrix) |
569+
| 3GLDM_DNN | Normalized dependence non-uniformity (grey level dependence matrix) |
570+
| 3GLDM_GLV | Gray level variance (grey level dependence matrix) |
571+
| 3GLDM_DV | Dependence variance (grey level dependence matrix) |
572+
| 3GLDM_DE | Dependence entropy (grey level dependence matrix) |
573+
| 3GLDM_LGLE | Low gray level emphasis (grey level dependence matrix) |
574+
| 3GLDM_HGLE | High gray level emphasis (grey level dependence matrix) |
575+
| 3GLDM_SDLGLE | Small dependence low gray level emphasis (grey level dependence matrix) |
576+
| 3GLDM_SDHGLE | Small dependence high gray level emphasis (grey level dependence matrix) |
577+
| 3GLDM_LDLGLE | Large dependence low gray level emphasis (grey level dependence matrix) |
578+
| 3GLDM_LDHGLE | Large dependence high gray level emphasis (grey level dependence matrix) |
579+
| 3GLDZM_SDE | Small distance emphasis (grey level distance zone matrix) |
580+
| 3GLDZM_LDE | Large distance emphasis (grey level distance zone matrix) |
581+
| 3GLDZM_LGLZE | Low grey level zone emphasis (grey level distance zone matrix) |
582+
| 3GLDZM_HGLZE | High grey level zone emphasis (grey level distance zone matrix) |
583+
| 3GLDZM_SDLGLE | Small distance low grey level emphasis (grey level distance zone matrix) |
584+
| 3GLDZM_SDHGLE | Small distance high grey level emphasis (grey level distance zone matrix) |
585+
| 3GLDZM_LDLGLE | Large distance low grey level emphasis (grey level distance zone matrix) |
586+
| 3GLDZM_LDHGLE | Large distance high grey level emphasis (grey level distance zone matrix) |
587+
| 3GLDZM_GLNU | Grey level non uniformity (grey level distance zone matrix) |
588+
| 3GLDZM_GLNUN | Normalized grey level non uniformity (grey level distance zone matrix) |
589+
| 3GLDZM_ZDNU | Zone distance non uniformity (grey level distance zone matrix) |
590+
| 3GLDZM_ZDNUN | Normalized zone distance non uniformity (grey level distance zone matrix) |
591+
| 3GLDZM_ZP | Zone percentage (grey level distance zone matrix) |
592+
| 3GLDZM_GLM | Grey level mean (grey level distance zone matrix) |
593+
| 3GLDZM_GLV | Grey level variance (grey level distance zone matrix) |
594+
| 3GLDZM_ZDM | Zone distance mean (grey level distance zone matrix) |
595+
| 3GLDZM_ZDV | Zone distance variance (grey level distance zone matrix) |
596+
| 3GLDZM_ZDE | Zone distance entropy (grey level distance zone matrix) |
597+
| 3GLRLM_SRE | Short run emphasis (grey level run length matrix) |
598+
| 3GLRLM_LRE | Long run emphasis (grey level run length matrix) |
599+
| 3GLRLM_GLN | Gray level non-uniformity (grey level run length matrix) |
600+
| 3GLRLM_GLNN | Normalized gray level non-uniformity (grey level run length matrix) |
601+
| 3GLRLM_RLN | Run length non-uniformity (grey level run length matrix) |
602+
| 3GLRLM_RLNN | Normalized run length non-uniformity (grey level run length matrix) |
603+
| 3GLRLM_RP | Run percentage (grey level run length matrix) |
604+
| 3GLRLM_GLV | Gray level variance (grey level run length matrix) |
605+
| 3GLRLM_RV | Run variance (grey level run length matrix) |
606+
| 3GLRLM_RE | Run entropy (grey level run length matrix) |
607+
| 3GLRLM_LGLRE | Low gray level run emphasis (grey level run length matrix) |
608+
| 3GLRLM_HGLRE | High gray level run emphasis (grey level run length matrix) |
609+
| 3GLRLM_SRLGLE | Short run low gray level emphasis (grey level run length matrix) |
610+
| 3GLRLM_SRHGLE | Short run high gray level emphasis (grey level run length matrix) |
611+
| 3GLRLM_LRLGLE | Long run low gray level emphasis (grey level run length matrix) |
612+
| 3GLRLM_LRHGLE | Long run high gray level emphasis (grey level run length matrix) |
613+
| 3GLRLM_SRE_AVE | directional average of 3GLRLM_SRE |
614+
| 3GLRLM_LRE_AVE | directional average of 3GLRLM_LRE |
615+
| 3GLRLM_GLN_AVE | directional average of 3GLRLM_GLN |
616+
| 3GLRLM_GLNN_AVE | directional average of 3GLRLM_GLNN |
617+
| 3GLRLM_RLN_AVE | directional average of 3GLRLM_RLN |
618+
| 3GLRLM_RLNN_AVE | directional average of 3GLRLM_RLNN |
619+
| 3GLRLM_RP_AVE | directional average of 3GLRLM_RP |
620+
| 3GLRLM_GLV_AVE | directional average of 3GLRLM_GLV |
621+
| 3GLRLM_RV_AVE | directional average of 3GLRLM_RV |
622+
| 3GLRLM_RE_AVE | directional average of 3GLRLM_RE |
623+
| 3GLRLM_LGLRE_AVE | directional average of 3GLRLM_LGLRE |
624+
| 3GLRLM_HGLRE_AVE | directional average of 3GLRLM_HGLRE |
625+
| 3GLRLM_SRLGLE_AVE | directional average of 3GLRLM_SRLGLE |
626+
| 3GLRLM_SRHGLE_AVE | directional average of 3GLRLM_SRHGLE |
627+
| 3GLRLM_LRLGLE_AVE | directional average of 3GLRLM_LRLGLE |
628+
| 3GLRLM_LRHGLE_AVE | directional average of 3GLRLM_LRHGLE |
629+
| 3GLSZM_SAE | Small area emphasis (grey level size zone matrix) |
630+
| 3GLSZM_LAE | Large area emphasis (grey level size zone matrix) |
631+
| 3GLSZM_GLN | Gray level non-uniformity (grey level size zone matrix) |
632+
| 3GLSZM_GLNN | Normalized gray level non-uniformity (grey level size zone matrix) |
633+
| 3GLSZM_SZN | Size-zone non-uniformity (grey level size zone matrix) |
634+
| 3GLSZM_SZNN | Normalized size-zone non-uniformity (grey level size zone matrix) |
635+
| 3GLSZM_ZP | Zone percentage (grey level size zone matrix) |
636+
| 3GLSZM_GLV | Gray level variance (grey level size zone matrix) |
637+
| 3GLSZM_ZV | Zone variance (grey level size zone matrix) |
638+
| 3GLSZM_ZE | Zone entropy (grey level size zone matrix) |
639+
| 3GLSZM_LGLZE | Low gray level zone emphasis (grey level size zone matrix) |
640+
| 3GLSZM_HGLZE | High gray level zone emphasis (grey level size zone matrix) |
641+
| 3GLSZM_SALGLE | Small area low gray level emphasis (grey level size zone matrix) |
642+
| 3GLSZM_SAHGLE | Small area high gray level emphasis (grey level size zone matrix) |
643+
| 3GLSZM_LALGLE | Large area low gray level emphasis (grey level size zone matrix) |
644+
| 3GLSZM_LAHGLE | Large area high gray level emphasis (grey level size zone matrix) |
645+
| 3NGLDM_LDE | Low dependence emphasis (neighbouring grey level dependence matrix) |
646+
| 3NGLDM_HDE | High dependence emphasis (neighbouring grey level dependence matrix) |
647+
| 3NGLDM_LGLCE | Low grey level count emphasis (neighbouring grey level dependence matrix) |
648+
| 3NGLDM_HGLCE | High grey level count emphasis (neighbouring grey level dependence matrix) |
649+
| 3NGLDM_LDLGLE | Low dependence low grey level emphasis (neighbouring grey level dependence matrix) |
650+
| 3NGLDM_LDHGLE | Low dependence high grey level emphasis (neighbouring grey level dependence matrix) |
651+
| 3NGLDM_HDLGLE | High dependence low grey level emphasis (neighbouring grey level dependence matrix) |
652+
| 3NGLDM_HDHGLE | High dependence high grey level emphasis (neighbouring grey level dependence matrix) |
653+
| 3NGLDM_GLNU | Grey level non-uniformity (neighbouring grey level dependence matrix) |
654+
| 3NGLDM_GLNUN | Grey level non-uniformity normalised (neighbouring grey level dependence matrix) |
655+
| 3NGLDM_DCNU | Dependence count non-uniformity (neighbouring grey level dependence matrix) |
656+
| 3NGLDM_DCNUN | Dependence count non-uniformity normalised (neighbouring grey level dependence matrix) |
657+
| 3NGLDM_DCP | Dependence count percentage (neighbouring grey level dependence matrix) |
658+
| 3NGLDM_GLM | Grey level mean (neighbouring grey level dependence matrix) |
659+
| 3NGLDM_GLV | Grey level variance (neighbouring grey level dependence matrix) |
660+
| 3NGLDM_DCM | Dependence count mean (neighbouring grey level dependence matrix) |
661+
| 3NGLDM_DCV | Dependence count variance (neighbouring grey level dependence matrix) |
662+
| 3NGLDM_DCENT | Dependence count entropy (neighbouring grey level dependence matrix) |
663+
| 3NGLDM_DCENE | Dependence count energy (neighbouring grey level dependence matrix) |
664+
| 3NGTDM_COARSENESS | Coarseness (neighbouring grey tone difference matrix) |
665+
| 3NGTDM_CONTRAST | Contrast (neighbouring grey tone difference matrix) |
666+
| 3NGTDM_BUSYNESS | Busyness (neighbouring grey tone difference matrix) |
667+
| 3NGTDM_COMPLEXITY | Complexity (neighbouring grey tone difference matrix) |
668+
| 3NGTDM_STRENGTH | Strength (neighbouring grey tone difference matrix) |
669+
670+
671+
## 3D feature groups
672+
------------------------------------
673+
| Group code | Belonging features |
674+
|--------------------|-------------|
675+
| \*3D_ALL\* | All the 3D features |
676+
| \*3D_ALL_INTENSITY\* | 3COV, 3COVERED_IMAGE_INTENSITY_RANGE, 3ENERGY, 3ENTROPY, 3EXCESS_KURTOSIS, 3HYPERFLATNESS, 3HYPERSKEWNESS, 3INTEGRATED_INTENSITY, 3INTERQUARTILE_RANGE, 3KURTOSIS, 3MAX, 3MEAN, 3MEAN_ABSOLUTE_DEVIATION, 3MEDIAN, 3MEDIAN_ABSOLUTE_DEVIATION, 3MIN, 3MODE, 3P01, 3P10, 3P25, 3P75, 3P90, 3P99, 3QCOD, 3RANGE, 3ROBUST_MEAN, 3ROBUST_MEAN_ABSOLUTE_DEVIATION, 3ROOT_MEAN_SQUARED, 3SKEWNESS, 3STANDARD_DEVIATION, 3STANDARD_DEVIATION_BIASED, 3STANDARD_ERROR, 3UNIFORMITY, 3UNIFORMITY_PIU, 3VARIANCE, and 3VARIANCE_BIASED |
677+
| \*3D_ALL_MORPHOLOGY\* | 3AREA, 3AREA_2_VOLUME, 3COMPACTNESS1 and -2, 3MESH_VOLUME, 3SPHERICAL_DISPROPORTION, 3SPHERICITY, 3VOLUME_CONVEXHULL, 3VOXEL_VOLUME, 3MAJOR_AXIS_LEN, 3MINOR_AXIS_LEN, 3LEAST_AXIS_LEN, 3ELONGATION, and 3FLATNESS |
678+
| \*3D_ALL_TEXTURE\* | All the 3GLCM_... 3GLDM_... 3GLDZM_... 3GLSZM_... 3GLRLM_... 3NGLDM_... and 3NGTDM_... features |
679+
| \*3D_GLCM\* | All the 3GLCM_... features |
680+
| \*3D_GLDM\* | All the 3GLDM_... features |
681+
| \*3D_GLDZM\* | All the 3GLDZM_... features |
682+
| \*3D_GLSZM\* | All the 3GLSZM_... features |
683+
| \*3D_GLRLM\* | All the 3GLRLM_... features |
684+
| \*3D_NGLDM\* | All the 3NGLDM_... features |
685+
| \*3D_NGTDM\* | All the 3NGTDM_... features |
686+
687+
454688
## Command line usage
455689

456690
Assuming you [built the Nyxus binary](#building-from-source) as outlined below, the following parameters are available for the command line interface:

0 commit comments

Comments
 (0)