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P41 Software and Resources

We are committed to sharing the software programs and supporting documentation developed by the Resource with biomedical researchers and educators.  All software and materials are copyright Vanderbilt University and free for use by non-profit academic institutions; see individual tool documentation for specific license information. Commercial licensing is available.  These tools are provided “as-is” and without support.

Source Code

Where source code is available, it is copyright Vanderbilt University and subject to license as described in code documentation. Generally, we use the GNU Public License for users in the non-profit sector, and the Limited GNU Public License (LGPL) for commercial development.

We expect and encourage researchers to modify our source code.  We will, at our discretion, integrate user-submitted code modifications without cost or royalties into our official release if their submissions comply with the GPL or similar license schemes.

Citation

We ask users of our tools to cite the specific Resource publications as noted in individual tool documentation when using Resource tool in your own research.

 

Tools

Molecular Image Fusion

The Molecular Image Fusion system is a software framework that can predict ion distributions in tissue. It accomplishes this by fusing data from two distinct technologies: imaging mass spectrometry (IMS) and microscopy. IMS-generated molecular maps, rich in chemical information but having coarse spatial resolution, are combined with optical microscopy maps, which have relatively low chemical specificity but high spatial information.

The Fusion Tool Prototype software package includes a command line utility that can be used to fuse user-provided data sets and an example multi-modal data set (IMS-microscopy on mouse brain) . For more information, download, and licensing requirements see the VU E-innovations web site.

If the Fusion Tool Prototype software package or its example data are used in a publication, cite Van de Plas R., Yang J., Spraggins J. & Caprioli R.M., Image fusion of mass spectrometry and microscopy: a multimodality paradigm for molecular tissue mapping, Nature Methods, advanced online publication (doi:10.1038/nmeth.3296).

MSRC Image Registration Toolbox

The MSRC Registration Toolbox is a software toolbox that helps achieve microscopy to MALDI IMS image registration using explicit laser ablation mark registration using autofluorescence microscopy. This approach is naïve to IMS ion images and achieves state of the art accuracy in microscopy-IMS registration as well as means to evaluate registration accuracy. This tool also provides an interface for histology-directed markup on autofluorescence microscopy images to Bruker flexImaging software for IMS. The toolbox performs linear and non-linear registration between microscopy images and does preprocessing of IMS data for registration, and IMS data extraction based on the resulting registration.

To download the toolbox, see installation instructions, license, and get more specific information, please go to its GitHub repository.

Fiducial Slide Designs for IMS

We have designed custom microscope slides for IMS which feature landmarks for instrument alignment, histology-directed analysis, and registration for multimodal image analysis. The designs provide multiple well targets with different diameters for calibration and normalization, including 200um, 300um, 400um, and 1.5mm diameters which are suitable for both automated spotting and hand pipetting. Features are designed to appear easily in instrument targeting cameras, and slides have maximum open working area to accommodate large tissue samples.  Production on plain or ITO glass using an inexpensive screen-printing process makes routine use possible.  Several designs are available to suit specific needs.

For more information and CAD drawings, please see our GitHub site.