M2aia-Interactive, fast, and memory-efficient analysis of 2D and 3D multi-modal mass spectrometry imaging data.

Jonas Cordes,Carsten Hopf,Thomas Enzlein,Sandy Engelhardt,Christian Marsching,Ivo Wolf,Marven Hinze

doi:10.1093/gigascience/giab049

Abstract

BackgroundMass spectrometry imaging (MSI) is a label-free analysis method for resolving bio-molecules or pharmaceuticals in the spatial domain. It offers unique perspectives for the examination of entire organs or other tissue specimens. Owing to increasing capabilities of modern MSI devices, the use of 3D and multi-modal MSI becomes feasible in routine applications—resulting in hundreds of gigabytes of data. To fully leverage such MSI acquisitions, interactive tools for 3D image reconstruction, visualization, and analysis are required, which preferably should be open-source to allow scientists to develop custom extensions.FindingsWe introduce M2aia (MSI applications for interactive analysis in MITK), a software tool providing interactive and memory-efficient data access and signal processing of multiple large MSI datasets stored in imzML format. M2aia extends MITK, a popular open-source tool in medical image processing. Besides the steps of a typical signal processing workflow, M2aia offers fast visual interaction, image segmentation, deformable 3D image reconstruction, and multi-modal registration. A unique feature is that fused data with individual mass axes can be visualized in a shared coordinate system. We demonstrate features of M2aia by reanalyzing an N-glycan mouse kidney dataset and 3D reconstruction and multi-modal image registration of a lipid and peptide dataset of a mouse brain, which we make publicly available.ConclusionsTo our knowledge, M2aia is the first extensible open-source application that enables a fast, user-friendly, and interactive exploration of large datasets. M2aia is applicable to a wide range of MSI analysis tasks.

Highlights

Imaging of molecular information in the spatial domain enables insights into otherwise hidden conditions and metabolic processes
We introduce M2aia (MSI applications for interactive analysis in Medical Imaging Interaction Toolkit (MITK)), a software tool providing interactive and memory-efficient data access and signal processing of multiple large Mass spectrometry imaging (MSI) datasets stored in imaging mz Markup Language (imzML) format
M2aia can be considered as an interactive open-source exploration and analysis application for MSI data with the capability of 3D image reconstruction and multi-modal image registration that is extensible by the community

Summary

Introduction

Imaging of molecular information in the spatial domain enables insights into otherwise hidden conditions and metabolic processes. 2 M2aia—Analysis of 2D and 3D multi-modal mass spectrometry imaging data cal and industrial applications It is a proven technique used for development of pharmacological agents [2] or for phenotyping of pathological tissue samples [3]. Mass spectrometry imaging (MSI) is a label-free analysis method for resolving bio-molecules or pharmaceuticals in the spatial domain. It offers unique perspectives for the examination of entire organs or other tissue specimens. Owing to increasing capabilities of modern MSI devices, the use of 3D and multi-modal MSI becomes feasible in routine applications—resulting in hundreds of gigabytes of data To fully leverage such MSI acquisitions, interactive tools for 3D image reconstruction, visualization, and analysis are required, which preferably should be open-source to allow scientists to develop custom extensions. M2aia is applicable to a wide range of MSI analysis tasks

Results

Discussion

Conclusion