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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.


Performs the four pre-processing tasks above resulting in a single 2D image of the stained manifold across which contrast is optimized and illumination is the same. PreMosa is able to detect and project the signals of interest, despite the presence of background noise. It uses a method that accurately aligns the planes even if their alignment is priorly unknown. The tool uses a particular order to pre-process individual tasks that allows it to reduce the required memory and computation time.


Offers a platform of pre-processing image tools. Scintillate is an open source software that allows users to evaluate time-series calcium imaging. It was developed with the aim of complementing the existing acquisition and pre-processing systems. The application includes a set of methods for detection and visualization of images. It can estimate the value of the sample being viewed, assess the viability of the preparation in seconds, spare microscope time, lamp hours and reduce distress to the subject.


Proposes a large collection of generic tools based on mathematical morphology to process binary and grey-level 2D and 3D images, integrated into user-friendly plugins. The library provides different categories of functions, corresponding to standard image processing workflows: (i) image processing and filtering; (ii) segmentation; (iii) post-processing; (iv) quantitative analysis; (v) library re-usability. The cell-resolved data provided by MorphoLibJ will be useful for the analysis of cell lineage, and the modelling of plant growth and morphogenesis in 3D.

SIMA / Sequential IMage Analysis

Facilitates common analysis tasks related to fluorescence imaging. Functionality SIMA includes correction of motion artifacts occurring during in vivo imaging with laser-scanning microscopy, segmentation of imaged fields into regions of interest (ROIs), and extraction of signals from the segmented ROIs. A graphical user interface (GUI) has also been developed for manual editing of the automatically segmented ROIs and automated registration of ROIs across multiple imaging datasets. This software has been designed with flexibility in mind to allow for future extension with different analysis methods and potential integration with other packages.


Determines regions of peak intensity into 2D and 3D images. FindFoci is a toolkit for ImageJ/J2 software that identifies potential foci and then, expands these into peaks that are gathered to finally remove the insignificant ones. It is composed of six algorithms including FindFoci GUI that allows parameters to be interactively updated. Additionally, the software includes six other plugins that extends features of the primary algorithm by permitting to compare regions of interest (ROI) points or align the identified foci.

Anisotropic Diffusion 2D

Serves for vector-valued image regularization. Anisotropic Diffusion 2D is a program based on variational methods and partial differential equations (PDEs). This tool consists in a single generic anisotropic diffusion equation that provides a simple interpretation of the regularization process in terms of local filtering with spatially adaptive Gaussian kernels. It also offers the possibility to specialize a generic expression into different regularization PDEs depending on different applications: flow visualization, image restoration, magnification, or inpainting.


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.


Stabilizes in vivo intravital microscopy images that suffer from soft-tissue background movement. StabiTissue quantifies the coincidence between image pairs from randomly distributed image regions. The method stabilizes the full 3D stack, aligning images within and across stacks. It provides an easy to use interface for the specific problem of stabilization. The method is more immune to noise and provides better performance for datasets’ possessing nonlinear tissue deformations.


Predicts the magnitude of errors in the data obtained from a confocal image based on information about microscope parameters used for the image acquisition. The main function of CorrectPattern is to correct errors due to pixel saturation in an input gene expression pattern. CorrectPattern can accurately correct the errors in data obtained from strongly clipped images, thereby allowing to obtain images of the higher dynamical range and thus to extract more detailed quantitative information from them. The method demonstrates high prediction accuracy and was applied for correction of errors in the data on segmentation gene expression in Drosophila blastoderm stored in the FlyEx database.

Attenuation correction

Allows users to perform attenuation correction for rectifying the fluorescence levels throughout the stack. Attenuation correction is an algorithm that relies on the assumption that the image background should be stationary throughout an image stack. The correction aims at rectifying the background average intensity and standard-deviation. The purpose of this operation is to make the average and standard-deviation of the background constant throughout the image stack.


Allows automatization of complex microscopy protocols. YouScope is an open-source microscope control platform for implementing complex measurement protocols. The software enables users to perform single-cell imaging as well as microplate imaging on a motorized light-microscope. It also provides a set of tools and configurable measurement types. The platform offers a large set of plug-in interfaces, allowing existing protocols to be extended, and allowing creation of new protocols from parts of existing ones.