A collection of useful code mainly for analyzing imaging data
The links are to our github repository. Used at your own risk please report any bugs and issues to r.mort@lancaster.ac.uk.
Web-based tools:
Evergene – Evergene is a user-friendly webtool developed by Barbara Shih’s group (Lancaster University) that utilises RNA-sequencing data, alongside other sample and clinical annotation, for large-scale gene-centric analysis, including principal component analysis (PCA), survival analysis (SA) and correlation analysis (CA).
ImageJ Toolsets:
Clonal Tools – ClonalTools are a set of macros designed for the analysis of mosaic patterns. The macros correct for the effects of random clumping using the formula 1/(1-p) devised by Roach (1968) in the way outlined by West (1975, 1976) and West et al (1997).
Mort R.L. Quantitative analysis of patch patterns in mosaic tissues with ClonalTools software. 2009. Journal of Anatomy. 215169870410.1111/j.1469-7580.2009.01150.x.
https://imagejdocu.list.lu/plugin/analysis/clonaltools/start?s[]=clonal
Fucci Tools – A simple ImageJ toolset for the analysis of Fucci cell cycle reporters in time lapse sequences.
Van Kerckwoorde, M., Ford, MF., Yeyati, PY., Mill P and Mort R. L. Live imaging and analysis of cilia and cell cycle dynamics with the Arl13bCerulean-Fucci2a biosensor and Fucci Tools. 2021. Cell Cycle Oscillators: Methods and Protocols, Methods in Molecular Biology. Springer.
Simi Reader – Simple tool to read Simi.sbd files created by Simi Biocell and analyze and plot the lineage tree in ImageJ.
Cell Patterning – is an ImageJ toolset comprising of a number of macros to aid in the analysis of cell movements during pattern formation (specifically hair follicle formation). It has only been tested on confocal timelapse sequences of cells labelled with nuclear marker Tcf/Lef:H2B-GFP.
Glover J.D., Wells K.L., Matthäus F., Painter K.J., Ho W., Riddell J., Johansson J.A., Ford M.J., Jahoda C.A.B., Klika V., Mort R.L., Headon D.J. Hierarchical patterning modes orchestrate hair follicle morphogenesis. 2017. PLoS Biology. 155 e200211710.1371/journal.pbio.2002117.
Well Detection – Tool to detect and analyse wells in PDMS microarrays specifically for identifying and analysing circular wells in a hyperstack image and linking them through time.
Useful bits of code (ImageJ, bash, Python in no particular order):
Autofocus Hyperstack – Selects the in-focus slice in each frame of a hyperstack and creates a new stack.
Tiled Autofocus – Divides the image into ROIs and selects the in-focus ROI across the slice in each frame of an ImageJ hyperstack – creates a new stack. For correcting slant in confocal Z-stacks.
Diffusion Analysis (Time Ensemble) – Performs a diffusion analysis using the time ensemble average method described in Charsooghi, MA et al 2011. Plots mean squared displacement against time from a results table of ImageJ tracking data. Inspect the fit – the diffusion coefficient (D) is the slope/4.
Charsooghi, M. A., Akhlaghi, E. A., Tavaddod, S. & Khalesifard, H. R. A MATLAB program to calculate translational and rotational diffusion coefficients of a single particle. Comput. Phys. Commun. 182, 400–408 (2011) .
Mort R.L., Ross R.J.H., Hainey K.J., Harrison O.J., Keighren M.A., Landini G., Baker R.E., Painter K.J., Jackson I.J., Yates C.A. Reconciling diverse mammalian pigmentation patterns with a fundamental mathematical model. 2016. Nature Communications. 741028810.1038/ncomms10288.
Stats from ImageJ Results-Example macro calculating stats from an ImageJ results table column.
Plot Zeroed Tracks – Example macro plotting ImageJ tracking data with a x/y = 0 origin.
Linux Virtual Machine Setup – A bash script to set up Lancaster University virtual Linux installations for Image Analysis.