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.
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