Analysis workflow for characterization of platelet spreading and morphology

This repository contains the workflows presented in Pike et al. (2020) [1]. If you use or adapt these workflows you should cite this publication. The workflows make extensive use of the open-source software platforms KNIME [2] and ilastik [3, 4]. More details and installation instructions can be found in the user guide (userGuide.pdf).

References

[1] Jeremy A Pike, Victoria A Simms, Christopher W Smith, Neil V Morgan, Abdullah O Khan, Natalie S Poulter, Iain B Styles, and Steve G Thomas. An adaptable analysis workflow for characterization of platelet spreading and morphology. bioRxiv, 2020.

[2] Michael R Berthold, Nicolas Cebron, Fabian Dill, Thomas R Gabriel, Tobias Kötter, Thorsten Meinl, Peter Ohl, Kilian Thiel, and Bernd Wiswedel. KNIME-the Konstanz information miner: Version 2.0 and beyond. AcM SIGKDD explorations Newsletter, 11(1):26–31, 2009.

[3] Christoph Sommer, Christoph Straehle, Ullrich Köthe, and Fred A Hamprecht. Ilastik: Interactive learning and segmentation toolkit. In 2011 IEEE International Symposium on Biomedical Imaging: From nano to macro, pages 230–233. IEEE, 2011.

[4] Stuart Berg, Dominik Kutra, Thorben Kroeger, Christoph N Straehle, Bernhard X Kausler, Carsten Haubold, Martin Schiegg, Janez Ales, Thorsten Beier, Markus Rudy, et al. ilastik: interactive machine learning for (bio) image analysis. Nature Methods, pages 1–7, 2019.