Centroid: The geometric centre of a nuclear compartment, when the compartment is non-spherical (e.g. chromosome territories) the center is usually taken as the intensity gravity centre.

Color image: For a RGB image, each pixel has a separate red, green and blue pixel value. Often the three different values are stored as three separate grayscale images (one for each of red, green and blue), which can be combined together when displaying or processing.

Hypothesis test:  A quantitative procedure for assessing some characteristic of the spatial distribution of compartments in the nucleus. This requires specification of a null hypothesis (often CSR, implying no organization).  The magnitude of a test statistic, like minimum inter-compartment distance, is then calibrated against its behaviour under the null hypothesis. Rejecting the hypothesis of CSR means that observed data supports some other random mechanism, such as clustering (often interpreted as attraction), regularity (often interpreted as inhibition) or spatial exclusion (for example, preferring the interior of the nucleus).

Image segmentation: Images are often segmented in order to separate out regions of the image corresponding to objects from those regions corresponding to background. Segmentation is determined by a single parameter known as the threshold value.

Monte Carlo A simulation strategy utilising pseudo-random numbers. Hypothesis tests calibrate the observed value of a test statistic against the sampling distribution of the statistic under an assumed null hypothesis. In cases where the sampling distribution cannot be exactly determined mathematically, Monte Carlo simulation may be used to obtain an approximation. 

Pixel value: Every pixel in an image has a pixel value or intensity indicating how bright that pixel is. For a grayscale image the pixel value is a single number with a range of possible values between 0 and 255, where 0 is black and 255 is white. Values between 0 and 255 make up the different shades of gray.

Radial Analysis/Peeling: An approach to hypothesis testing that involves partitioning the nuclear volume into non-overlapping, contiguous regions. The test statistic compares the observed numbers of compartments in each region with the expected numbers under some null hypothesis, often CSR.

Random: the location of a compartment is random if it cannot be precisely specified prior to observing the nucleus. Common use is taken to imply that any location is equally likely [see uniformity].

Resolution: the minimum distance measurable between two points.

Spatial point processes: a spatial point process is a mechanism that locates compartments in the nucleus in a random manner.  The property of Complete Spatial Randomness (CSR) describes a mechanism that locates compartments such that any location in the nucleus is equally likely (that is, uniformly). CSR is often used as a model for lack of organisation in formal statistical procedures [see hypothesis test]

Thresholding: A specified pixel value is chosen as the threshold value. During thresholding, pixels in the image lower than the threshold value are set to 0 (or black) and pixels higher than the threshold are set to 255 (or white). For color images, different threshold values can be specified for red, green and blue.

Uniformity: The uniform distribution assigns the same probability to regions of equal size. In terms of the spatial distribution of compartments, (with some technical assumptions), a uniform spatial distribution would be take to mean CSR

Voxel: A volume element, the three dimensional analogue of a pixel.