Image registration software tools | Mass spectrometry imaging analysis
Mass spectrometry imaging (MSI) provides high quality data for understanding and visualize the spatial distribution of chemical compounds in biological samples. However, many imaging modalities (e.g., fluorescence microscopy, whole slide imaging) brings alternative crucial information. In order to compile those data, image registration comes as the image processing solution. Image registration is also useful to compare different conditions between tissue samples.
Assists users with multiple imaging mass spectrometry (IMS) analyses. RegCombIMS was developed to co-register, combine and create single IMS datasets acquired from serial sections of tissue. This package allows for automation of the process and identification of species that are not detected together but spatially colocalized after registration. This method also permits users to correlate ions from IMS acquisitions that require incompatible sample preparations.
A vendor-neutral interface built on the Matlab platform designed to view and perform data analysis of Mass Spectrometry Imaging (MSI) data. A standalone version of MSiReader for which Matlab is not required is also provided. People who are unfamiliar with the Matlab language will have little difficulty navigating the user friendly interface, and users with Matlab programming experience can adapt and customize MSiReader for their own needs.
A comprehensive bioinformatics tool for MALDI tissue imaging, facilitates data processing, visualization and analysis of spatial distribution of individual ions across the sampled locations on a tissue section. The program accepts imaging mass spectrometric data in standard file formats. MALDIVision generates an ion intensity map for any m/z in the analysis range, enabling simultaneous imaging of many compounds. Users can view images in 2-D and in 3-D.
Performs 2D image registration based on elastic deformations represented by B-splines. bUnwarpJ is an ImageJ plugin that works on registration of two images, A and B: Image A is elastically deformed to look as similar as possible to image B, and, at the same time, the "inverse" transformation (from B to A) is also calculated. As a result, two images are given: the deformed versions of A and B images.
Performs image segmentation and registration. CMP-BIA is dedicated to ImageJ/Fiji and contains a plugin named jSLIC. This plugin is a segmentation method for clustering, in a given image, similar regions (as known as superpixels) which are usually used for other segmentation techniques, classification and registration. It gives reliable superpixels shapes, with no need of decreasing their size.
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