Image segmentation software tools | Mass spectrometry imaging analysis
Mass Spectrometric Imaging (MSI) is a molecular imaging technique that allows the generation of 2D ion density maps for a large complement of the active molecules present in cells and sectioned tissues. Automatic segmentation of such maps according to patterns of co-expression of individual molecules can be used for discovery of novel molecular signatures (molecules that are specifically expressed in particular spatial regions).
Assists users to analyze mass spectrometry imaging data. SCILS Lab includes a lot of functionalities allowing researchers to display multiple samples in both 2D and 3D and permitting a multitude of applications in pharmaceutical, medical, and industrial research. This software is composed of several features among which comparative analysis for uncovering discriminative m/z-markers, classification model calculation based on training data and classification of new samples, or extraction of underlying trends.
A mass spectrometry imaging toolbox for statistical analysis. Cardinal is an R package that implements statistical and computational tools for analyzing mass spectrometry imaging datasets, including methods for efficient pre-processing, spatial segmentation, and classification.
Allows users to analyze and process images captured with NanoSIMS 50 & 50L secondary ion mass spectrometers (Cameca). OpenMIMS is an ImageJ plugin that is developed for biomedical research. This tool is able to open, treat and save stacks of images for up to 7 different isotopes. Image ratios and Hue-Saturation-Intensity (HSI) maps of any combination of isotopes can be displayed. Moreover, it can display all data from any number of Regions of Interest (ROIs) extracted, analyzed and tabulated for single images.
Organizes and processes multimodal mass spectrometry imaging data. HDI Software allows users to interrogate complex imaging data. The software enables the integration of multimodal imaging experiments for SYNAPT G2-Si as well as DESI imaging for Xevo G2-XS Mass Spectrometers. Some of its benefits are the image clarity and integrity, as well as Sequential sample acquisition for accelerated throughput.
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.
Segments nearly elliptic objects via parametric active contour. E-Snake applies an active contour (named snake) segmentation method by using exponential splines as basis functions to represent the outline of the shape. This ImageJ plugin emulates elliptical and circular shapes and can produce an approximation of any closed curve in the plane. These proprieties can be useful to delineate cross sections of cylindrical-like conduits and to outline blob-like objects.