Morphology measurement software tools | Mass spectrometry imaging analysis

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 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.

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.

Calculates standard bone histomorphometry parameters on a digitized trabecular-bone surface, according to the parallel plates model. Map_BoneMicrostructure is an ImageJ plugin for calculating bone area fraction (BA/TA), trabecular thickness (TbTh), trabecular separation (TbSp) and trabecular number per length unit (TbN). The software processes 8-bit grayscale images with black-colored bone-trabeculae on white background.

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.