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.
Turns raw photo-activated localization microscopy data into three-dimensional super-resolved images. Palm3d is a data-processing program that processes in 6 steps: (i) construct a calibration stack; (ii) identify candidate particles in each data image; (iii) localize each candidate particle using the calibration stack; (iv) correct for drift; (v) optionally, link localizations and re-localize and (vi) construct image histograms from localization data.
Permits advanced analysis of single-molecule localization microscopy (SMLM) data. VividSTORM employs the unbiased active contour selection of the labeled profile to measure intermolecular distances within identified axon terminals in dual-channel stochastic optical reconstruction microscopy (STORM) data. It can be useful for correlated analysis of pixel intensity–based and localization microscopy data.
Provides a user-friendly means of visualizing, filtering and analyzing localization microscopy (LM) data. PALMsiever includes drift correction, clustering, intelligent line profiles, many rendering algorithms, and 3D data visualization. It incorporates the main analysis and data processing modalities used by experts in the field, as well as several new features we developed, and makes them broadly accessible. It can easily be extended via plugins and is provided as free of charge open-source software.
Allows local density estimation, segmentation and quantification of 3D single-molecule localization microscopy (SMLM) data. voronoi3D was validated using simulated and experimental data, illustrating its applicability to different biological objects of interest. It can be used to quantify 3D information such as spatial organization, local density, volume and shape of labelled protein clusters in 3D and number of molecules within a given cluster.
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