ap-browning / Spheroids

Data, code and interactive figures for the preprint "Quantitative analysis of tumour spheroid structure”.

Spheroids

Repository for the paper "Quantitative analysis of tumour spheroid structure" available on eLife.

Figures

• Figure 1
• Figure 3
• Figure 4
• Figure 5
• Figure 6
• Figure A1
• Figure A2
• Figure A3
• Figure S3

Data

All data used in the analysis is available in Data. Data collected from the Incucyte S3 (Satorius) (i.e., outer radius measurements only) is available in IncucyteData.csv. Data summarised from confocal microscopy images (find the repository containing image processing codes here) is available in AllConfocalData.csv. Data are processed using code available at https://github.com/ap-browning/SpheroidsImageProcessing.

The script SubsetData.jl randomly subsets the complete confocal data set in Data/AllConfocalData.csv so that the sample size for each condition is approximately the same (a random seed is used to ensure reproducability).

The datasets contain the following variables

Variable	Values	Description
CellLine	983b or 793b	Cell line
InitialCondition	2500, 5000, 10000	Initial number of cells in each spheroid.
Day	Number	Days elapsed between spheroid seeding and measurement.
R	Number	Spheroid outer radius.
φ	Number ∈ [0,1]	Proportion of outer radius containing inhibited or dead cells.
η	Number ∈ [0,1]	Proportion of outer radius void of living cells.

Running the code

Installation

Code to produce all results is contained within this repository, including the Julia modules Greenspan and Inference. To download, first clone this Github repo. Next, add the two module folders to your LOAD_PATH:

push!(LOAD_PATH,"/path/to/repo/Module/Greenspan")
push!(LOAD_PATH,"/path/to/repo/Module/Inference")

Next, run the following code (press ] to enter the Pkg REPL) to install all required packages and activate the project

(v1.6) pkg> activate .
(Spheroids) pkg> instantiate

Results

Code used to produce each figure in the main document and supplementary material is available in the Figures folder. For example, to reproduce Figure 4, run Figures/Figure 4/fig4.jl. This will create a plot stored in the variable fig4 that contains Figure 4.

Note that most figures contain a version saved as html. While these figures may differ stylistically from those in the main document, opening these in a web browser allows for interaction with the figure.

Citation

If you use the data or software in this repository in your own work, please cite the following:

AP Browning, JA Sharp, RJ Murphy, G Gunasingh, B Lawson, K Burrage, NK Haass, MJ Simpson. 2021 Quantitative analysis of tumour spheroid structure. eLife 10:e73020 doi:10.7554/eLife.73020

@article{Browning.2021gh,
	title        = {Quantitative analysis of tumour spheroid structure},
	author       = {Browning, Alexander P and Sharp, Jesse A and Murphy, Ryan J and Gunasingh, Gency and Lawson, Brodie and Burrage, Kevin and Haass, Nikolas K and Simpson, Matthew J},
	year         = 2021,
	volume       = 10,
	pages 	     = {e73020},
	journal      = {eLife},
	doi          = {10.7554/eLife.73020}
}