BioMap PDF Print E-mail

' contains all the functions I could think of and many more which are extremely useful...'.

Rich featured biomedical image analysis software.

Supported Image Formats Analyze 7.5, TIF, DICOM, PNP
Requirements Windows, Unix, Linux or MAC OS (new) with IDL RT 6.1 or higher
Origin, Copyright Novartis
Author Martin Rausch, MSI additions by Markus Stoeckli
Download (6 MB) (3 MB, update from 3.8.0 and above, copy biomap.sav to BioMap\bin directory)
Demo Data (1 MB)
Registration Online


With the development of the MALDI Mass Spectrometric Imaging Technology the availability of a powerful processing and displaying software became a crucial factor. With BioMap we have now a tool available which was originally developed for the evaluation of MRI data in biomedical research. It was modified over the years (1996 till now) to support many more imaging modalities, including optical, PET, CT, NIRF and MSI.

BioMap was written in IDL™. It provides a common visualization and storage platform, which can be used for visualization of data from any source, provided that an import filter exists for this format. This platform can be extended by various software packages, individually designed for analysis of specific data sets. Visualization is based on multi-planar reconstruction allowing extraction of arbitrary slices from a 3D-volume. Other features linked to visualization are overlying of two individual data sets or displaying of ROIs. BioMap uses a 4-dimensional representation of imaging data. The first three dimensions are used for describing the position of a voxel in space, the fourth dimension is reserved for independent parameters such as time, mass, wavelength or diffusion weighting. In addition to the voxel data, a header is used to store information for scan identification, the physical position of the object in space (important for co-registration of multiple scans) or the imaging protocol. Image data can be imported from several sources. Processed data, however, will always be stored in Analyze-format. This format was used since it is widely distributed and can be loaded by several other tools, like ANALYZE (Mayo clinics) or SPM (Welcome department of cognitive neurology, London). BioMap comprises all tools, which are required to process single-subject-data, to combine results from several subjects or sessions and to document the final result of a study. Import and export of partially processed data to other software-tools can therefore be avoided.




To maintain the compatibility with Unix/Linux and Windows there is no automatic setup routine available. Follow the instructions in the included 'readme.txt' file.

Documentation, Training

BioMap contains an extremely rich function set which is only partly described in the manual. There are many 'tricks' which are not obvious to first-time users. We suggest that you learn from your colleagues or that you check the forum for training opportunities.


Short movies demonstrating MSI data analysis with BioMap: