Windows

Super-resolution optical fluctuation imaging (SOFI) achieves 3D super-resolution by computing temporal cumulants or spatio-temporal cross-cumulants of stochastically blinking fluorophores. In contrast to localization microscopy, SOFI is compatible with weakly emitting fluorophores and a wider range of blinking conditions. Balanced SOFI analyses several cumulant orders for extracting molecular parameter maps, such as the bright and dark state lifetimes, the concentration and the brightness distributions of fluorophores within biological samples. In combination with a deconvolution of the cumulant images, the estimated parameter maps proved useful to balance the image contrast and to linearize the brightness and blinking response. Thereby, the image quality and the resolution were improved significantly.

The MorphoLeaf application allows you to extract the contour of multiple leaf images and identify their biologically-relevant landmarks. These landmarks are then used to quantify morphological parameters of individual leaves and to reconstruct average leaf shapes. MorphoLeaf is developed by the Modeling and Digital Imaging and the Transcription Factors and Architecture teams of the Institut Jean-Pierre Bourgin, INRA Versailles, France, and the Biophyscis and Development group at RDP, Lyon.

Free-D is a three-dimensional (3D) reconstruction and modeling software. It allows to generate, process and analyze 3D point and surface models from stacks of 2D images. Free-D is an integrated software, offering in a single graphical user interface all the functionalities required for 3D modeling. It runs on Linux, Windows, and MacOS. Free-D is developed by the Modeling and Digital Imaging team of the Institut Jean-Pierre Bourgin, INRA Versailles, France.

SuReSim (Super Resolution Simulation) is an open-source simulation software for Single Molecule Localization Microscopy (SMLM). The workflow of the SuReSim algorithm starts from a ground truth structure and lets the user choose to either directly simulate 3D localizations or to create simulated *.tiff-stacks that the user can analyze with any given SMLM reconstruction software. A 3D structure of any geometry, either taken from electron microscopy, designed de-novo from assumptions or known structural facts, is fluorophore-labeled in silico. A defined set of parameters is used to calculate and visualize the 3D localizations of the corresponding labels. The software package is accompanied with a library of model structures that can be imported and simulated. Users manual with tutorial provided.

arivis Vision4D is a modular software for working with multi-channel 2D, 3D and 4D images of almost unlimited size independent of available RAM. Many imaging systems, such as high speed confocal, Light Sheet/ SPIM and 2 Photon systems, can produce a huge amount of multi-channel data, which arivis Vision4D handles without constraints. Terabyte ready arivis Vision4D main functionality: Easy import of most image formats from microsopes as well as biological formats High performance interactive 3D / 4D rendering on standard PCs and laptops with 3D Graphics Support Intuitive tools for stitching and alignment to create large multi-dimensional image stacks Immediate 2D, 3D and 4D visualization, annotation and analysis regardless of image size Creation, import, and export of 4D Iso-surfaces Powerful Analysis Pipeline for 3D /4D image analysis (cell segmentation, tracking, annotation, quantitative measurement and statistics, etc) Semi-automatic/manual segmentation and tracking with interactive Track Editor Easy design and export of 3D / 4D High Resolution Movies Seamless integration of custom workflows via Matlab API and Python scripting Data sharing for collaboration A user friendly software, easy to learn and use for any life scientist