Automated

This plugin allows : Calculating co-localization between objects in 3D Measuring 3D distances between nearest object, co-localized or not Getting some 3D measurements about each objects The plugin can be used with labelled images, but it also integrates tools for the segmentation of the objects. Programming language: JAVA Processes: Denoise filter Segmentation of the objects Object based co-localization and distance analysis Counting and measurements on objects

This is the source code and data page of a distributed parallel algorithm 2683 for segmentation of large fluorescence microscopy images.

Image-processing algorithms developed at the MOSAIC Group for fluorescence microscopy. Tools included:

• 2D/3D single-particle tracking tool which can be used to track bright spots in 2D/3D movies over time.
• Optimal filament segmentation of 2D images. 
• Curvature filters for image filtering, denoising, and restoration. 
• Image naturalization for image enhancement based on gradient statistics of natural-scence images. 
• Tool for automatically send and distribute jobs on clusters and get back the results.
• Multi-region image segmentation of 2D and 3D images without needing to know the number of regions beforehand. 
• Squassh for globally optimal segmentation of piecewise constant regions in 2D and 3D images and for object-based co-localization analysis. 
• Tool for inferring spatial interactions between patterns of objects in images or between coordinates read from a file.
• Tool for robust, histogram-based background subtraction well suited to correct for inhomogeneous illumination artifacts.
• A tool to estimate the Point-Spread Function of the microscopy out of 2D fluorescence images.
• A tool to measure the 3D Point-Spread Function of a confocal microscope from an image stack.
• Addition of synthetic Poisson-distributed noise to an image in order to simulate shot noise of various signal-to-noise ratios. 
• Convolution of an image with a Bessel function in order to simulate imaging with a microscope. 
• A utility to detect bright spots in images and estimate their center. 
• A utility to create manual segmentations to be used as ground truth to test and benchmark automatic segmentation algorithms.
• A tool for replacing one color in an image with another color.

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.