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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.


Provides an algorithm for the estimation and correction of errors in quantitative gene expression levels obtained from blurred confocal images. StepDeconvolution is a modification of the Richardson-Lucy method that provides more precise restoration of the data which is read from blurred images of objects with sharp edges. Quantification of confocal images is implemented by means of image segmentation procedure that determines nuclear borders and constructs the binary mask of an image. The mask is applied to a gene expression image so that the information is only read from intranuclear areas and intensity values are averaged over all the pixels composing the nucleus.

Fast Multilevel Thresholded-Landweber Deconvolution Algorithm

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.