Analyzes, processes and visualizes multi-dimensional microscopy images. BioImageXD puts open-source computer science tools for three-dimensional visualization and analysis into the hands of all researchers, through a user-friendly graphical interface tuned to the needs of biologists. BioImageXD has no restrictive licenses or undisclosed algorithms and enables publication of precise, reproducible and modifiable workflows. It allows simple construction of processing pipelines and should enable biologists to perform challenging analyses of complex processes.
Assists in deconvolution of 2D and 3D images corrupted by Poisson noise. SGP-dec is a Matlab package that computes a deconvolved image by early stopping the scaled gradient projection (SGP) algorithm. This method was developed for the solution of the optimization problem coming from the minimization of the generalized Kullback-Leibler divergence between the blurred image and the observed image.
Provides a tool for 3D deconvolution of images from widefield, confocal, two-photon, light sheet and high content analysis (HCA) microscopes. Microvolution adjusts blurring and minimizes the effect of noise by using an inverse of the point spread function (PSF) to each point of the measured image. It is available as an ImageJ or µManager plug-in and is compatible with MetaMorph. A direct integration is possible through an API version.
A Python package for deconvolving 3D microscope images. IOCBio Microscope collects all necessary elements for deconvolution using the Richardson–Lucy algorithm with total variation regularization. This includes, reading microscope images of various formats (TIFF, RAW and LSM files), estimating PSF from the measurements of microspheres, deconvolving images with different algorithm options, etc.
Assists in managing deconvolution problems with a wavelet-domain regularization. Fast Multilevel Thresholded-Landweber Deconvolution Algorithm can reduce a quadratic data term to a regularization on the L1-norm of the wavelet coefficients of the solution. This software shows slow convergence for ill-conditioned operators arising for example in deconvolution. It makes wavelet-regularized deconvolution more accessible including with limited software.
Reconstructs and makes complex datasets easily accessible. BigStitcher is an ImageJ plugin that enables interactive visualization, precise alignment, real-time fusion, deconvolution, support for alignment of multi-tile acquisition taken from different physical orientations, or so-called multi-tile views. It can also be used for doubling the size of specimens that can be imaged, while further orthogonal views can render the resolution isotropic.
Restores images from microscopic data. Huygens is based on the deconvolution approach that reassigns out-of-focus light to its origin, thus improves signal-to-noise in images. It can use physically-acquired or simulated point-spread functions (PSFs) for characterization of optical system being deconvolved. The tool shows high-performance in in-house tests on deconvolution compared to other software packages. It provides intuitive wizards for parameter selection and processing.
Allows deconvolution and visualization of image sets. AutoQuant is a package of 2D and 3D restoration algorithms that permits users to improve the resolution and contrast of images that have undergone distortions during the image acquisition process, for thus improving their analysis. Users can choose the algorithm that fits their requirements.
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