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MiCASA / Multitaper Circularly Averaged Spectral Analysis

Detects statistically robust phenotypic differences. MiCASA is an unbiased, user-independent method for identifying the phenotypic differences between conditions. It focuses attention on those aspects of the phenotype that have statistical relevance. This package may be used to provide a useful summary of the distribution and interactions between well-known cell types in the thymus. However, MiCASA can be used with any pair of markers.


A software application on MATLAB to visualize surface data from 3D fluorescence microscopy. Map3-2D accurately accurately projects up to five-dimensional (5D) fluorescence microscopy image data onto full-content 2D maps. Similar to the Earth's projection onto cartographic maps, Map3-2D unfolds surface information from a stack of images onto a single, structurally interconnected map. By cross-referencing between the 2D map and the original image stack, precise quantitative analyses of intensities and shapes are easily and intuitively executable.

Spectral Imaging Toolbox

Measures accurately cell membrane lipid packing without cytosolic contributions using a single dye. The Spectral Imaging Toolbox was designed for spectral analysis of high magnification images of single or sub-confluent cells, vesicles and microbubbles. This method permits to process and analyze a dataset containing over 1500 cells in a few hours. It also addresses a growing need to process large spectral imaging datasets and data from experiments with multiple exposures.


Allows preprocessing and subsequent multivariate analysis of spectral imaging data. SpectralAnalysis is an analysis software that can be used through the entire analysis workflow, for data sets acquired from single experiments to large multi-instrument, multimodality, and multicenter studies. The software enables testing of algorithms with instant visualization of the results. It is suitable for comparisons of preprocessing methods on mass spectrometry imaging (MSI) data acquired on any instrument.

Amira 3D Software for Life Sciences

Allows users to visualize, manipulate, and understand data from imaging modalities such as computed tomography, microscopy or Magnetic resonance imaging (MRI). Amira 3D Software for Life Sciences provides features to import and process 2D and 3D images data, visualization techniques and tools for visual analysis. Users can also create and share presentations. The base product can be customized by adding functional extensions to fit special needs in different application areas.