A collection of useful code mainly for analysing imaging data. Links go to our GitHub repository. Used at your own risk — please report bugs to r.mort@lancaster.ac.uk.
Teaching materials
Introduction to ImageJ — introductory slide deck covering the basics of ImageJ for image analysis.
Web-based tools
Evergene — a user-friendly web tool developed by Barbara Shih’s group (Lancaster University) for large-scale gene-centric analysis of RNA-sequencing data, including PCA, survival analysis and correlation analysis.
ImageJ toolsets
Fucci Tools — a simple ImageJ toolset for the analysis of Fucci cell cycle reporters in time-lapse sequences.
Van Kerckwoorde M, Ford MJ, Yeyati PY, Mill P, Mort RL. Live imaging and analysis of cilia and cell cycle dynamics with the Arl13bCerulean-Fucci2a biosensor and Fucci Tools. Cell Cycle Oscillators: Methods and Protocols, Methods in Molecular Biology. Springer. 2021.
Clonal Tools — a set of macros for the analysis of mosaic patterns, correcting for random clumping using the formula devised by Roach (1968) as outlined by West (1975, 1976) and West et al. (1997).
Mort RL. Quantitative analysis of patch patterns in mosaic tissues with ClonalTools software. Journal of Anatomy. 2009. doi:10.1111/j.1469-7580.2009.01150.x
Cell Patterning — an ImageJ toolset for analysing cell movements during pattern formation, specifically hair follicle formation. Tested on confocal time-lapse sequences labelled with Tcf/Lef:H2B-GFP.
Glover JD, Wells KL, Matthäus F, Painter KJ, Ho W, Riddell J, Johansson JA, Ford MJ, Jahoda CAB, Klika V, Mort RL, Headon DJ. Hierarchical patterning modes orchestrate hair follicle morphogenesis. PLoS Biology. 2017. doi:10.1371/journal.pbio.2002117
Simi Reader — reads Simi .sbd files created by Simi Biocell, and analyses and plots the lineage tree in ImageJ.
Well Detection — detects and analyses wells in PDMS microarrays, identifying and analysing circular wells in a hyperstack image and linking them through time.
Utility scripts
Autofocus Hyperstack (ImageJ) — selects the in-focus slice in each frame of a hyperstack and creates a new stack.
Tiled Autofocus (ImageJ) — divides the image into ROIs and selects the in-focus ROI across each frame of a hyperstack. Useful for correcting slant in confocal Z-stacks.
Diffusion Analysis (Time Ensemble) (ImageJ) — performs diffusion analysis using the time ensemble average method of Charsooshi et al. 2011. Plots mean squared displacement against time from ImageJ tracking data; the diffusion coefficient D is the slope/4.
Charsooshi MA, Akhlaghi EA, Tavaddod S, Khalesifard HR. A MATLAB program to calculate translational and rotational diffusion coefficients of a single particle. Comput. Phys. Commun. 2011;182:400–408.
Stats from ImageJ Results (ImageJ) — example macro calculating statistics from an ImageJ results table column.
Plot Zeroed Tracks (ImageJ) — example macro plotting ImageJ tracking data with an x/y = 0 origin.
Linux Virtual Machine Setup (bash) — a script to set up Lancaster University virtual Linux installations for image analysis.