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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.
Enables the visualization, analysis of large data sets. msIQuant allows users to display and study data sets without data reduction. It has a quantitation function that generates calibration standard curves from series of standards that can be used to determine the concentrations of specific analyses. In summary, it supplies solution for accessing and evaluating data sets, quantifying drugs and endogenous compounds in tissue areas of interest, and for processing mass spectra and images.
Serves for interactive and in-depth analysis of mass spectrometry imaging data. MassImager contains three subsystems: MassImager Solution, MassImager Visualization and MassImager Intelligence. The core design is aimed at user-friendly design, high throughput, instrument-independence, interactive visualization, various multivariate statistical analysis and pattern recognition of large mass spectrometry imaging (MSI) dataset. The tools provided by the MassImager solution can be classified in two categories: visual processing and image analysis.
Generates 2D/3D images for the elements present in a set from inductively coupled plasma-mass spectrometry (ICP/MS) spectra. LA-iMageS is a fast and automatic generation of high-quality elemental distribution bioimages in the PerkinElmer Elan XL format, whose results can be directly exported to external applications for further analysis. Ultimately, it can produce a link with different fields of scientific research (metallomics, medicine, biology, environmental and geology among others), enabling a suitable pace for transdisciplinary collaborations.
Enables construction, manipulation, analysis and comparison of mass spectrometry (MS) images. MSight is designed for 2-D representation, as well as visual analysis and comparison of datasets obtained from protein or peptide separation combined to MS. The software allows navigation through large volumes of data and provides visualization tools to discriminate peptide or protein from noise or to perform differential analysis. It aims to improve understanding of correlated high-throughput MS.
A collection of R scripts for the efficient evaluation of .imzML archives in a four-step strategy: (1) calculation of the density distribution of mass-to-charge ratio (m/z) signals in the .imzML file and assembling of a pseudo-master spectrum with peak list, (2) automated generation of mass images for a defined scan range and subsequent visual inspection, (3) visualisation of individual ion distributions and export of relevant .mzML spectra and (4) creation of overlay graphics of ion images and photographies. The use of a Hue-Chroma-Luminance (HCL) colour model in MSI graphics takes into account the human perception for colours and supports the correct evaluation of signal intensities. Further, readers with colour blindness are supported. Contour maps promote the visual recognition of patterns in MSI data, which is particularly useful for noisy data sets.
DCE / Datacube Explorer
Studies and displays 2D mass spectrometry imaging (MSI) datasets. DCE allows the visualization of data stored in the BioMap data format, imzML and the Datacube format. It is able to investigate large MSI data sets, without dealing with computer programming. This tool loads ion intensity data of the MSI dataset into a virtual datacube allowing fast search and retrieval of image data. It summarizes all ion intensities of the mass bins inside a requested mass window per individual pixel of the image.
Allows visualization of characteristics of liquid chromatography–mass spectrometry (LC-MS) measurements. rawDiag is an R package that supports LC-MS operators during the process of empirical method optimization. The software acts as an interface to vendor specific software libraries that can access the spectrum-level metadata contained in a mass spectrometer measurement. This software provides several plot functions tailored towards mass spectrometry data. rawDiag can be customized and implemented into more complex environments.
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.
OpenMIMS / Open Multi-isotope Imaging Mass Spectrometry
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.
An open source web- and MATLAB-based software tool for both DESI and MALDI mass spectrometry imaging (MSI) that performs computationally intensive functions on a remote server. These functions include converting data from a variety of file formats into a common format easily manipulated in MATLAB, transforming time-series mass spectra into mass spectrometry images based on a probe spatial raster path, and multivariate analysis. OmniSpect provides an extensible suite of tools to meet the computational requirements needed for visualizing open and proprietary format MSI data.