Spectre is a versatile tool used for analysis of MALDI-MSI data sets.
For the sake of simplicity, the toolset provided is available to be used through web application interface, which is currently a work-in-progress.
This is the legacy MATLAB code we started from, with original implementations of algorithms.
The project is currently in its early stage. However, it comprises the implementation of unique spectra modelling based on Gaussian Mixture Models, and Divisive IK-means algorithm for unsupervised segmentation, which can be used for efficient dataset compression, as well as for knowledge discovery. Aformentioned algorithms have already been published and refering links have been enclosed under references section.
Please contact us by e-mail. We will answer you in details.
Short contribution guide is actively constructed on the project's wiki as the development progresses.
This software is part of contribution made by Data Mining Group of Silesian University of Technology, rest of which is published here.
- Marczyk M, Polanska J, Polanski A: Comparison of Algorithms for Profile-Based Alignment of Low Resolution MALDI-ToF Spectra. In Advances in Intelligent Systems and Computing, Vol. 242 of Man-Machine Interactions 3, Gruca A, Czachorski T, Kozielski S, editors. Springer Berlin Heidelberg 2014, p. 193-201 (ISBN: 978-3-319-02308-3), ICMMI 2013, 22-25.10.2013 Brenna, Poland
- P. Widlak, G. Mrukwa, M. Kalinowska, M. Pietrowska, M. Chekan, J. Wierzgon, M. Gawin, G. Drazek and J. Polanska, "Detection of molecular signatures of oral squamous cell carcinoma and normal epithelium - application of a novel methodology for unsupervised segmentation of imaging mass spectrometry data," Proteomics, vol. 16, no. 11-12, pp. 1613-21, 2016
- M. Pietrowska, H. C. Diehl, G. Mrukwa, M. Kalinowska-Herok, M. Gawin, M. Chekan, J. Elm, G. Drazek, A. Krawczyk, D. Lange, H. E. Meyer, J. Polanska, C. Henkel, P. Widlak, "Molecular profiles of thyroid cancer subtypes: Classification based on features of tissue revealed by mass spectrometry imaging," Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics, 2016
- G. Mrukwa, G. Drazek, M. Pietrowska, P. Widlak and J. Polanska, "A Novel Divisive iK-Means Algorithm with Region-Driven Feature Selection as a Tool for Automated Detection of Tumour Heterogeneity in MALDI IMS Experiments," in International Conference on Bioinformatics and Biomedical Engineering, 2016
- A. Polanski, M. Marczyk, M. Pietrowska, P. Widlak and J. Polanska, "Signal partitioning algorithm for highly efficient Gaussian mixture modeling in mass spectrometry," PloS one, vol. 10, no. 7, p. e0134256, 2015