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.
In order to build and run the application, please refer to the install section of the main repository.
Please note, that this repository contains just a subset of several components the Spectre project has been divided into. To view the main repository and to consult its readme, please refer to this page.
The native-algorithms repository encapsulates the C++ implementations of the Gaussian Mixture Modelling and Genetic algorithms used for the sake of fast and efficient computations. The Gaussian Mixture Modelling is expected to have its CUDA implementation carried out in near future.
Aformentioned algorithms have already been published and refering links have been enclosed under references section.
Also, several classification and clusterization methods will be provided soon, along with supporting statistics.
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