Table 1.
This table lists all of the nuclear texture features measured for both chromatin organization and H3K9 spatial expression [26, 27]. Many ofthese are second- and third-order statistical calculations (e.g. Haralick features [26]) from the spatial domain. These allow the measurement of subvisual features not visible to the naked eye in addition to spatial alterations readily visible as changes in chromatin organization
| Abbreviation | Texture feature description |
|---|---|
| Geometric features | |
| Area | Area occupied by nucleus |
| Ellipsea | Major axis length |
| Ellipseb | Minor axis length |
| Perim | Perimeter of the nucleus |
| Feretmin | Minimum ferret length |
| Feretmax | Maximum ferret length |
| Feretratio | Ratio of ferret length |
| Fcircle | Form circle |
| Dcircle | Equivalent circle |
| Densitimetric features | |
| Meand | Mean optical density within the nucleus |
| Stdd | Standard deviation of mean optical densities |
| Skewd | Skewness of optical densities (distribution around the mean) |
| Kurtd | Kurtosis of optical densities (extremes from the mean) |
| Energyd | Uniformity of chromatin |
| Entropyd | Disorganization of chromatin |
| Mind | Minimum optical density within the nucleus |
| Maxd | Maximum optical density within the nucleus |
| Sumd | Sum of the optical densities within the nucleus |
| Sumqd | Sum of squared optical densities within the nucleus |
| Haralick features | |
| Haram 1–11 | Mean values in four principle directions (Haralick) |
| Harar 1–11 | Range values in four principle directions (Haralick) |
| DISCRETE FEATURES | |
| LDarea | Area covered by low-density regions within the nucleus (Doudkine) |
| MDarea | Area covered by medium-density regions within the nucleus (Doudkine) |
| HDarea | Area covered by high-density regions within the nucleus (Doudkine) |
| Lamount | Proportion of sum optical density due to low-density regions (Doudkine) |
| Mamount | Proportion of sum optical density due to medium-density regions (Doudkine) |
| Hamount | Proportion of sum optical density due to high-density regions (Doudkine) |
| LVM | Comparison of mean optical densities of low-density regions with those of medium-density regions (Doudkine) |
| LVH | Comparison of mean optical densities of low-density regions with those of high-density regions (Doudkine) |
| LVMH | Comparisons of mean optical densities of low-density regions with those of medium and high-density regions (Doudkine) |
| LDO | Number of low-density objects (Doudkine) |
| MDO | Number of medium-density objects (Doudkine) |
| HDO | Number of high-density objects (Doudkine) |
| LDC | Compactness (shape) of low-density regions (Doudkine) |
| MDC | Compactness (shape) of medium-density regions (Doudkine) |
| HDC | Compactness (shape) of high-density regions (Doudkine) |
| MHDC | Compactness (shape) of medium and high-density regions (Doudkine) |
| LAD | Average distance of low-density regions from the geometric centre of the nucleus (Doudkine) |
| MAD | Average distance of medium-density regions from the geometric centre of the nucleus (Doudkine) |
| HAD | Average distance of high-density regions from the geometric centre of the nucleus (Doudkine) |
| MHAD | Average distance of medium and high-density regions from the geometric centre of the nucleus (Doudkine) |
| LCOM | Distance between the centre of mass of low-density regions and the geometric centre of the nucleus (Doudkine) |
| MCOM | Distance between the centre of mass of medium-density regions and the geometric centre of the nucleus (Doudkine) |
| HCOM | Distance between the centre of mass of high-density regions and the geometric centre of the nucleus (Doudkine) |
| MHCOM | Distance between the centre of mass of medium and high regions and the geometric centre of the nucleus (Doudkine) |