TY - JOUR

T1 - Numerical experiments with MALDI Imaging data

AU - Kobarg, Jan Hendrik

AU - Mass, Peter

AU - Oetjen, Janina

AU - Tropp, Oren

AU - Hirsch, Eyal

AU - Sagiv, Chen

AU - Golbabaee, Mohammad

AU - Vandergheynst, Pierre

PY - 2014/6/1

Y1 - 2014/6/1

N2 - This article does not present new mathematical results, it solely aims at discussing some numerical experiments with MALDI Imaging data. However, these experiments are based on and could not be done without the mathematical results obtained in the UNLocX project. They tackle two obstacles which presently prevent clinical routine applications of MALDI Imaging technology. In the last decade, matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) has developed into a powerful bioanalytical imaging modality. MALDI imaging data consists of a set of mass spectra, which are measured at different locations of a flat tissue sample. Hence, this technology is capable of revealing the full metabolic structure of the sample under investigation. Sampling resolution as well as spectral resolution is constantly increasing, presently a conventional 2D MALDI Imaging data requires up to 100 GB per dataset. A major challenge towards routine applications of MALDI Imaging in pharmaceutical or medical workflows is the high computational cost for evaluating and visualizing the information content of MALDI imaging data. This becomes even more critical in the near future when considering cohorts or 3D applications. Due to its size and complexity MALDI Imaging constitutes a challenging test case for high performance signal processing. In this article we will apply concepts and algorithms, which were developed within the UNLocX project, to MALDI Imaging data. In particular we will discuss a suitable phase space model for such data and report on implementations of the resulting transform coders using GPU technology. Within the MALDI Imaging workflow this leads to an efficient baseline removal and peak picking. The final goal of data processing in MALDI Imaging is the discrimination of regions having different metabolic structures. We introduce and discuss so-called soft-segmentation maps which are obtained by non-negative matrix factorization incorporating sparsity constraints.

AB - This article does not present new mathematical results, it solely aims at discussing some numerical experiments with MALDI Imaging data. However, these experiments are based on and could not be done without the mathematical results obtained in the UNLocX project. They tackle two obstacles which presently prevent clinical routine applications of MALDI Imaging technology. In the last decade, matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) has developed into a powerful bioanalytical imaging modality. MALDI imaging data consists of a set of mass spectra, which are measured at different locations of a flat tissue sample. Hence, this technology is capable of revealing the full metabolic structure of the sample under investigation. Sampling resolution as well as spectral resolution is constantly increasing, presently a conventional 2D MALDI Imaging data requires up to 100 GB per dataset. A major challenge towards routine applications of MALDI Imaging in pharmaceutical or medical workflows is the high computational cost for evaluating and visualizing the information content of MALDI imaging data. This becomes even more critical in the near future when considering cohorts or 3D applications. Due to its size and complexity MALDI Imaging constitutes a challenging test case for high performance signal processing. In this article we will apply concepts and algorithms, which were developed within the UNLocX project, to MALDI Imaging data. In particular we will discuss a suitable phase space model for such data and report on implementations of the resulting transform coders using GPU technology. Within the MALDI Imaging workflow this leads to an efficient baseline removal and peak picking. The final goal of data processing in MALDI Imaging is the discrimination of regions having different metabolic structures. We introduce and discuss so-called soft-segmentation maps which are obtained by non-negative matrix factorization incorporating sparsity constraints.

U2 - 10.1007/s10444-013-9325-0

DO - 10.1007/s10444-013-9325-0

M3 - Article

SP - 667

EP - 682

JO - Advances in Computational Mathematics

JF - Advances in Computational Mathematics

SN - 1019-7168

ER -