Morphology measurement software tools | Mass spectrometry imaging analysis
Mass spectrometry imaging (MSI) was developing fast with the invention of various in-situ ionization sources and their combinations with different mass analyzers for specific analytical demands. The greatest power of MSI lies in its ability to simultaneously acquire the molecule features and their morphological distributions in one single MSI experiment. Nowadays, it has become the most promising analytical tool in the field of life science, metabolomics, proteomics, drug development, clinical diagnosis and molecular mechanism research.
Provides an easy-to-use tool for two-dimensional peptide and protein imaging of cells or tissue extracts. flexImaging provides comprehensive visualization of the spatial distribution of biomarker candidates in a tissue – thus greatly increasing the possibilities of biomarker analysis.
Offers a platform for fractal analysis and morphology functions. FracLac is a module that can be used as an ImageJ or FIJI plugin. The application includes features such as: (i) analyzing complexity and heterogeneity, (ii) measuring difficult to describe geometrical forms; (iii) extracting of pattern from several types of images for analysis. The software is suitable for images of biological cells as well as for other structures such as branching structures or known fractals.
Makes to physically interpret spectral and directional reflectance fields as sampled by Earth observation sensors in terms of leaf biochemical contents and canopy architecture. SAIL is coupled with PROSPECT and the numerical inversion of the resulting PROSAIL. It provides a means to generate databases and test new spectral indexes. It performs sensitivity analyses that will allow better designs on forthcoming sensors devoted to specific applications, long before their launch.
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.
Shows the calculation of emissivity, vegetation cover, reflectance, brightness temperature and radiance as a function of leaf area index (LAI). SAIL enables users to partly bridge the current gap between the analytical canopy–soil models operating separately in the optical and the thermal-infrared (TIR) spectral domains. It might lead to better exploitation of the possible synergies offered by simultaneous co-registered optical and TIR remote sensing observations.
MSI has emerged as a technique suited to resolving metabolism within complex cellular systems; where understanding the spatial variation of metabolism is vital for making a transformative impact on science. Unfortunately, the scale of MSI data and complexity of analysis presents an insurmountable barrier to scientists where a single 2D-image may be many gigabytes and comparison of multiple images is beyond the capabilities available to most scientists. The OpenMSI project will overcome these challenges, allowing broad use of MSI to researchers by providing a web-based gateway for management and storage of MSI data, the visualization of the hyper-dimensional contents of the data, and the statistical analysis.
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.