Paper BI+AI+AS+BA+IA+NL+NS+SP-WeA8
Tools For TOF-SIMS Image Analysis

Wednesday, October 30, 2013, 4:20 pm, Room 201 B

The use of time-of-flight secondary ion mass spectrometry (ToF-SIMS) for imaging has increased in recent years. This is due to the improvements in spatial resolution and ion yields from modern primary ion sources. These improvements have made ToF-SIMS attractive for cell and tissue imaging, especially due to the fact that ToF-SIMS can detect and identify a wide range of membrane lipids and other cellular components, and can potentially image these in both 2D and 3D. Characterization of tissues and cells by ToF-SIMS often requires advanced data collection and analysis methodologies including the use of stage rastering for large area analysis and 3D depth profiling. It is also often of interested to localize specific areas within a cell or tissue and carry out region of interest (ROI) analysis. Finally, ToF-SIMS image analysis presents challenges due to the shear size of the data sets. In order to deal with these large, complex data sets, we have created a set of Matlab toolboxes for multivariate analysis of both images and spectra. This talk will highlight new tools in the NBtoolbox that enable the user to process stage raster images, overlay images, and extract ROI images based off of image masks created from any imported image.

For example, the stage raster tools enable the user to import and run PCA on an entire stage raster image, or to dice the stage raster into separate image tiles that can then be analyzed individually. The ROI generation tools enable the user to import any image to be used as a ROI mask. Examples will be shown using florescent images from confocal microscopy as masks to extract ROI from ToF-SIMS images of mouse muscle tissue. Tools are also included for image alignment, and image cropping. All data processed with these tools can be analyzed using PCA, MAF or MCR.