A model of the spatial tumour heterogeneity in colorectal adenocarcinoma tissue

BMC Bioinformatics

Table 1 Parameters of the model. [ ^∗ can be variable, depending on real data and magnification level. ^† typical ranges for 1000 ×1000 pixels image with 40 × magnification, L _max=0.6, ν _e=ν _s=1]

Description	Annotation	Source	Typical values
Image size	i _h×i _w	User-defined	1000×1000
Magnification		User-defined	40 ×, 20 ×
Size of CCD pixel		User-defined	11 μ m
Size of scalebar		User-defined	10 μ m
Cancer grade	S	User-defined	{0, 1, 2, 3}
Cellularity of epithelial cells	ν _e	User-defined	[0, 1]
Cellularity of stromal cells	ν _s	User-defined	[0, 1]
Cell overlap	L _max	User-defined	[0, 1]
Variance of point spread function	G	User-defined	1 pixel
Variance of the CCD detector noise	σ _G	User-defined	0.00025
Stain matrix		User-defined
Distribution of nuclei major axis length	μ _l,σ _l	H&E data	^∗ μ m
Distribution of nuclei minor axis length	μ _w,σ _w	H&E data
Distribution of crypt minor axis length	μ _b,α _b, β _b	H&E data	^∗ μ m
Distribution of crypt ratio between axes	α _e,β _e	H&E data
Distribution of cell phenotypes		H&E data
Approximate cell radius	r	[22]	6μ m
Fraction of sample taken by crypts	f _c	Eq. 2	[0, 1]
Number of crypts	N _c	Eq. 1
Rotation of crypts	ϕ	Random	[0,2π]
Cell shape α,β	Eq. 10	α=0.1(S+1),β=0.05
Number of epithelial cells	N _e	Eq. 8	[110,200]^∗,†
Number of stromal cells	N _s	Eq. 7	[150,260]^∗,†
Total number of cells	N	Eq. 9	[340,380]^∗,†

ISSN: 1471-2105