Some computational tools and software produced by COMPARE research groups. Here we link to computation tools, please contact the relevant groups for further information and remember to cite the tools if they are used in publications and other outputs.
RSMLM
Contact: Jeremy Pike, j.a.pike@bham.ac.uk
Code: https://github.com/JeremyPike/RSMLM and https://github.com/JeremyPike/RSMLM-tutorials
Citation: Pike, J.A., Khan, A.O., Pallini, C., Thomas, S.G., Mund, M., Ries, J., Poulter, N.S. and Styles, I.B., 2020. Topological data analysis quantifies biological nano-structure from single molecule localization microscopy. Bioinformatics, 36(5), pp.1614-1621.
A R package for pointillist analysis of single molecule localization microscopy (SMLM) data. This package includes methods for persistence-based clustering (ToMATo), alongside DBSCAN, Voronoi tessellation and Ripley's K based clustering. There is also the capacity to simulate dSTORM data. Tutorials available as Binder ready Jupyter notebooks.
KNIME Analysis workflow for characterization of platelet spreading and morphology
Contact: Jeremy Pike, j.a.pike@bham.ac.uk
Code: https://github.com/JeremyPike/platelet-segmentation
Citation: Pike, J.A., Simms, V.A., Smith, C.W., Morgan, N.V., Khan, A.O., Poulter, N.S., Styles, I.B. and Thomas, S.G., 2021. An adaptable analysis workflow for characterization of platelet spreading and morphology. Platelets, 32(1), pp.54-58.
KNIME workflows for the segmentation and characterization of platelets. The workflow combines user placed markers with an ilastik pixel classifier to achieve cellular segmentation of densely packed cells. A random forest classifier in then used to classify platelets into user defined classed (e.g. spread/not-spread).