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.
An interactive, freely available, cross-platform 3D localization representation tool. ViSP advances the interpretation of 3D single-particle super-resolution data (and the features are also compatible with 2D data sets). With an ever-growing number of 3D microscopy techniques and applications available, the features that ViSP offers are of critical importance in the greater microscopy research community.
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.
Analyzes and quantifies 3D information of 3D single-molecule localization microscopy (SMLM) data. 3DClusterViSu can obtain spatial organization, local density, volume and shape of labelled protein clusters in 3D and number of molecules within a given cluster. It is applicable to different biological objects of interest such as fine chromatin structures in a dense cellular context. This tool is based on mathematical properties of 3D Voronoi diagrams.
Calculates the fractal dimensionality of a 3D structure. calcFD is designed to work with intermediate files from FreeSurfer analysis pipeline, but can also use other volumes. The toolbox includes options to use different masking files and is implemented to use either the box-counting or dilation algorithms and to use either the filled volume or just the surface of the structure. The toolbox can easily be run on all of the participants in a FreeSurfer subject folder, or just on specified subject folders. The Matlab toolbox also includes several functions designed to improve functionality, such as the automatic ‘cropping’ of the volume space to the smallest bounding box necessary to contain the volume, improving computation time drastically. Example files are also provided to aid in using the toolbox for the user‘s needs.
Integrates current global statistic methods. JACoP is a colocalization analysis tool which combines currently used colocalization methods and an object-based tool named three-dimensional (3D) object counter as plugins to the public domain ImageJ software. In order to simplify its utilization, this tool includes a many functions allowing users to select image side-by-side.
Allows the extraction of junctions, centerlines and filament lengths of biopolymer networks in 2D and 3D images. SOAX provides users a solution to analyze quantitatively, reproductively, and objectively the image data. It uses the stretching open active contours (SOACs) method to initialize automatically images. This tool permits 3D visualization in order to visually check results against the image and to explore image data.
Creates super-resolution (SR) models of virus nanoarchitecture. VirusMapper assists users in detecting, segmenting, aligning, classifying and averaging large datasets of individual viruses. It can resolve nanoscale changes in virus architecture and can be applied to multiple super-resolution modalities. This tool supports data such as structured illumination microscopy (SIM) or high-quality single-molecule localization microscopy (SMLM) with the requested labelling and localization density. It can be executed through ImageJ or Fiji and is part of the NanoJ project.
Calculates and plots the practical localization accuracy measure (PLAM). MUMDesignTool offers a user-friendly framework for finding the appropriate number of planes and plane spacings for a multifocal plane microscopy (MUM) setup. It also provides two working modes called “rapid” (noise-free) and “precise” (corrupted by background, stochastic signal amplification and readout noise). This application is capable of exporting the results and acquisition parameters as image and text files.
A pipeline for the reconstruction of discontinuous neuronal morphology in noisy images. SparseTracer is based on two methods. One is the region-to-region connection (RRC) method for detecting the initial part of a neurite, which can effectively gather local cues, i.e., avoid the whole image analysis, and thus boosts the efficacy of computation. The other is constrained principal curves method for completing the neurite reconstruction, which uses the past reconstruction information of a neurite for current reconstruction and thus can be suitable for tracing discontinuous neurites. SparseTracer is able to deal with the large-scale image dataset.
An extension of the DAOPHOT analysis method to the analysis of astigmatism-based 3D super-resolution data where the z position of the emitter is encoded in the x and y width of its point spread function (PSF). 3D-DAOSTORM simultaneously fits multiple overlapping images of adjacent emitters with different PSF shapes.
An automatic tracing framework for neuron reconstruction that does not require substantial human intervention. SmartTracing algorithm has been implemented as a plugin of Vaa3D, which is the common platform to implement algorithms for the BigNeuron project bench-testing. SmartTracing does not require human input of training exemplars and can self-adapt to different types of neuroimage data. Additionally, the method can be applied to improve the performance of other existing tracing methods.
Allows users to investigate the structure of large populations of viruses. MiLeSIM measures virus population heterogeneity by coupling methods of super-resolution microscopy (SRM), machine learning (ML)-based classification and image analysis. The application is suited for examining large numbers of particles with high specificity. It can be applied to virus-based biotechnology industry such as vaccine development.
Allows users to manage image data, results and derived data, and image analysis protocols. Imaris permits to tag resources as a search across all experiments or a specific set of experimental groups. It contains several features allowing to: (1) visualize volume images and objects, (2) identify objects according to their morphology, intensity, and more, (3) validate segmentation, (4) interact with objects, (5) create pictures and stunning animations.
Serves for visualizing electron tomography data. Tomviz can utilize the large quantities of memory and processing resources required to render, manipulate, and analyze voluminous 3D tomograms. It provides a graphical user interface (GUI) where objects can be rendered as shaded contours or volumetric projections. This tool also offers a set of functions such as multiple datasets, colormaps, and other visualization settings.
Allows users to visualize, manipulate, and understand data from imaging modalities such as computed tomography, microscopy or Magnetic resonance imaging (MRI). Amira 3D Software for Life Sciences provides features to import and process 2D and 3D images data, visualization techniques and tools for visual analysis. Users can also create and share presentations. The base product can be customized by adding functional extensions to fit special needs in different application areas.
Contains functionalities for processing and analysis image data. GoFigure2 is a platform which allows users to visualize and navigate through 4D multichannels bio-images. Besides, it aims to provide an automatic segmentation of nuclei and cell membranes and to enable the way of extracting data from bio-images.
Automatically and accurately locates neurons, which is helpful for neuronal dendritic tracing. NeuroGPS locates the cell body by computing the radius of each soma, and finding the most preferred radius and its corresponding coordinates. This method efficiently eliminates the interference from the complicated neurites, especially the thick dendritic truck, on localization, and is robust to the diverse shape, size, and density of neurons.
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