Shape Space Explorer is a software package in MATLAB. It uses a machine learning approach to understand the relationship of cell shape dynamics and cell migration behaviour. Our algorithm analyses cell shape from image timelapse sequences and learns the intrinsic low-dimensional structure of cell shape space. The resultant shape space map can be used to visualise differences in cell shape distribution following perturbation experiments and to analyse the quantitative relationships between shape and migration behaviour. The core of our software is a new, rapid, landmark-free shape difference measure that allows unbiased analysis of the widely varying morphologies exhibited by migrating epithelial cells.

If you use our software please cite the paper (link coming soon)

The developers of Shape Space Explorer are grateful to the developers of the following tools which are used in this software package:

Bio-Formats

Melissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782. doi: 10.1083/jcb.201004104

Edison MATLAB Interface

Shai Bagon, Weizmann Centre of Artificial Intelligence

EDISON

D. Comanicu, P. Meer: “Mean shift: A robust approach toward feature space analysis”. IEEE Trans. Pattern Anal. Machine Intell., May 2002.

P. Meer, B. Georgescu: “Edge detection with embedded confidence”. IEEE Trans. Pattern Anal. Machine Intell., 28, 2001.

C. Christoudias, B. Georgescu, P. Meer: “Synergism in low level vision”. 16th International Conference of Pattern Recognition, Track 1 - Computer Vision and Robotics, Quebec City, Canada, August 2001.

ProgressBar

Stefan Doerr (2012). Progress bar for matlab loops (incl. parfor) (https://www.mathworks.com/matlabcentral/fileexchange/43872-progress-bar-for-matlab-loops-incl-parfor), MATLAB Central File Exchange.

Spider

Michael Arant (2008). spider(data,tle,rng,lbl,leg,f) (https://www.mathworks.com/matlabcentral/fileexchange/22708-spider-data-tle-rng-lbl-leg-f), MATLAB Central File Exchange.

pmtk3

Matt Dunham, Kevin Murphy et al. (2019) Machine Learning: a Probabilistic Persepctive by Kevin Patrick Murphy, MIT Press (2012).