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Support for Large MALDI IMS Data Files

MALDI imaging mass spectrometry is known for its ability to specifically pinpoint ions of interest for further investigation. A low spatial resolution covers a larger tissue area but with lesser details on ion localization. However, a higher resolution can provide greater detail over a smaller area of the tissue section, potentially directed by histological analysis. A high spectral resolution results in large data which needs an efficient system for data storage, processing, ion map reconstruction and related analysis. MALDIVision can analyze large data sets running up to 5 GB, making the program tailored for analyzing high resolution MALDI tissue imaging experiments.

Data Processing

For ion map reconstruction, MALDIVision accepts experimental m/z and intensity values along with the co-ordinate information obtained from rastering a tissue slide. It enables specifying an m/z range which includes the metabolite of interest. You can specify the mass bin (0-2 Da) to reconstruct images with greater precision. The program accepts Analyze 7.5 and imzML format files as input datasets. No matter what make your instrument is, the output can be converted to imzML format using third party tools.

Comprehensive Image Display

To assist users in analyzing and processing MALDI tissue imaging data, the images are presented under two tabs, Frame and Multidimensional. Under the Frame tab, a user can create multiple frames for the same dataset, allowing comparative analysis of the spatial distribution of different ions of interest. The Multidimensional tab displays the mass spectra of the region of interest selected from the reconstituted image. MALDIVision facilitates manipulation of reconstituted images by actions such as zoom in/out, scroll, rotate and flip vertically or horizontally. Users can also define their own custom color theme and apply it to tissue images for better ion distribution rendering.

Normalized Image Display

MALDIVision generates normalized spatial distribution of a target compound based on a standard compound in the tissue. This enables users to visualize the relative abundance of the target compound with respect to a standard compound in regions of interest in the sampled tissue.

Co-register and Overlay Image

For a histological interpretation, combining MALDI IMS and classic histological staining provides researchers with a better diagnoses. MALDIVision facilitates users to co-register and overlay a MALDI image over an optical image facilitating accurate investigation of spatial distribution of a compound of interest. Additionally, up to 10 images can be overlaid.

Import Tissue Optical Image

MALDIVision can import optical images facilitating easy comparison of tissue sections with the ion intensity maps presented in 2D and 3D. The optical images can be imported in .jpeg, .tiff and .gif formats.

Extract Ion Image

MALDIVision facilitates reconstruction of image showing spatial distribution of a compound by extracting a specific mass from the mass spectrum. The reconstructed image of such extracted ion is termed as Extracted Ion Image (EII) and provides users a means to display the distribution of a compound of a specific mass observed on the mass spectrum.

Define Region of Interest

MALDIVision enables defining the Region of Interest (ROI) using different geometrical shapes. A user can define a single or multiple ROIs on the 2D ion intensity maps. The ROIs can be highlighted using color and labeled for easy identification. The program also enables users to view the averaged mass spectrum for a region of interest along with the statistics of the ion intensity distribution. Specific regions on a tissue image can be masked (hidden) or highlighted to assist in better analysis and visualization of the molecular spatial distribution in the tissue.

View Histogram and Cumulative Probability Graph

Users can generate a histogram and a cumulative probability graph to observe the ion intensity distribution in the defined ROI. The probability that the observed intensity level in the ROI is less/ greater than or equal to a specified level is displayed along with the ion intensity distribution statistics.

Export Ion Intensity Maps

MALDIVision enables exporting of ion intensity maps generated at specific m/z values. The maps can be exported as .tiff or .jpeg files for comparing ion distribution or sharing information with colleagues or as high resolution images for publishing results. The program simultaneously exports images for each one of the observed ions.

Project Management

MALDIVision provides a comprehensive project management setup, associating reconstituted tissue ion intensity maps with MALDI imaging mass spectrometry data and their corresponding optical images. You can create any number of projects. Each project can load multiple MALDI tissue imaging data files with a provision to create sessions within each loaded dataset. The projects can be classified on the basis of the tissue types, expected metabolites or research goals. This facilitates convenient handling of large datasets generated by MALDI tissue imaging experiments in an organized manner which always has been a challenge associated with the technology.

A Comprehensive Data Processing and Visualization Software for MALDI Imaging Mass Spectrometric Data

Matrix Assisted Laser Desorption Ionization Imaging Mass Spectrometry (MALDI IMS) is a promising new technology for visualizing the spatial distribution of analytes viz., proteins, peptides, lipids, drug candidate compounds and biomarkers present in a sampled tissue section. MALDI tissue imaging enables researchers to visualize multiple molecular distributions across the surface of a sample without the need for chemical labels or antibodies. MALDI IMS has been increasingly used for candidate biomarker discovery, drug metabolite profiling, lipid analysis and proteomics. MALDI tissue imaging contributes significantly towards disease diagnosis and is now being used to address a number of clinical questions in diseases such as cancer and organ development.

To apply MALDI Imaging technology for clinical purposes, it is essential to develop a computationally powerful data processing and visualization informatics tool which can aid in successful analysis of the large data files obtained during an experimental run.


  • Support for Large MALDI IMS Data Files
  • Data Processing
  • Comprehensive Image Display
  • Normalized Image Display
  • Co-register and Overlay Image
  • Import Tissue Optical Image
  • Extract Ion Image
  • Define Region of Interest
  • View Histogram and Cumulative Probability Graph
  • Export Ion Intensity Maps
  • Project Management


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