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.
Analyses data in which many overlapping fluorophores undergo bleaching and blinking events, giving the structure at enhanced resolution. By using a hidden Markov model (HMM), 3b allows useful information to be obtained from data that would be impossible to analyse with standard localisation analysis techniques.
Quantifies image quality in super-resolution microscopy. Squirrel produces a quantitative map of super-resolution artifacts and metrics and proposes to users optimizing imaging parameters. This ImageJ module offers the possibility to combine super-resolution renderings of the same structure to avoid overall error contributions. It features also Fourier Ring Correlation (FRC) for the mapping of resolution across super-resolution images.
Provides a complete set of tools for automated processing, analysis and visualization of data acquired by single-molecule localization microscopy (SMLM) methods. ThunderSTORM is a program that offers many different processing and post-processing methods so that users can adapt the analysis to their data. It is able to process the data using any combination of the implemented feature enhancing, spot detection and fitting methods.
Allows to work on both fixed-cell and dynamic live-cell super resolution using conventional fluorophores compatible with a variety of imaging modalities. SRRF provides a significant reduction in reconstruction artefacts, such as the disappearance of structures or ringing effects while remaining computationally efficient. It permits virtually any laboratory access to super-resolution imaging.
Serves for effective segmentation of multidimensional datasets. MIB can recognize several number of imaging formats and offers a variety of image processing tools. It also simplifies utilization and quantification of acquired data. It permits users to segment large datasets, to realize 3D visualization, and to quantify images and models. Its parameters enable users to insert plugin s to customize the program for specific needs.
An interactive open-source software with a graphical user interface, which allows performing processing steps for localization data in an integrated manner. This includes common features and new tools such as correction of chromatic aberrations, drift correction based on iterative cross-correlation calculations, selection of localization events, reconstruction of 2D and 3D datasets in different representations, estimation of resolution by Fourier ring correlation, clustering analysis based on Voronoi diagrams and Ripley’s functions. SharpViSu is optimized to work with eventlist tables exported from most popular localization software. The functionality of SharpViSu is extendable via plugins, such as ClusterViSu for comprehensive cluster analysis of localization microscopy data. It includes tools such as calculations of Voronoi and Ripley statistics with Monte-Carlo simulations, different modes of reconstruction (e.g. based on Gaussian blur or Ripley’s functions) and segmentation of density maps, retrieval of geometrical properties of detected clusters, segmentation based on Voronoi tessellation.
Offers an assortment of methods for quality assessment of structured illumination microscopy (SIM) data. SIMcheck supplies a wide range of features dedicated to: (i) resolution and image quality evaluation, (ii) detection of errors sources and artifacts, (iii) calibration simplification and (iv) image management including a converter. The application accepts raw and reconstructed data from various commercial SIM platforms including ImageJ.
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.
Improves the resolution of conventional fluorescent microscopy by one order of magnitude. SimpleSTORM is based on a carefully designed yet simple model of the image acquisition process which allows you to standardize each image such that the background has zero mean and unit variance. This standardization makes it possible to detect spots by a true statistical test (instead of hand-tuned thresholds) and to de-noise the images with an efficient matched filter.
Assists researchers in restoring fluorescence microscopy data. CSBDeep is a module that allows users to apply neural networks to image restoration tasks such as denoising, surface projection, recovery of isotropic resolution or the restoration of sub-diffraction structures. The software can be installed as part of the Fiji software or incorporated in KNIME workflows. Moreover, a simulation can be run through a Paperspace server for authorized users.
A full set of MATLAB routines as a guide to localization image processing. These routines can be used to perform the image processing element of localization microscopy, and includes resolution analysis. Additional scripts are included to perform : image simulation for testbenching and validation ; batch processing of multiple files ; fiducial marker tracking and drift correction ; chromatic offset correction ; and molecular trajectory imaging.
Restores images from microscopic data. Huygens is based on the deconvolution approach that reassigns out-of-focus light to its origin, thus improves signal-to-noise in images. It can use physically-acquired or simulated point-spread functions (PSFs) for characterization of optical system being deconvolved. The tool shows high-performance in in-house tests on deconvolution compared to other software packages. It provides intuitive wizards for parameter selection and processing.
Offers a collection of filters for 3D images supported by Java Native Interface. FastFilter3D performs several 3D filtering on 8-bits and 16-16-bits gray-levels stacks. This ImageJ plugin performs the following 3D filters: median, mean, minimum, maximum, maximum local and topchat.
Represents an integrated solution for data analysis and acquisition. SymPhoTime 64 permits users to target principally the results rather than the data processing. The interface of this tool simplifies the utilization by the user for an individual analysis or measurement process. Different data acquisition modes including interleaved trains of excitation and stimulated emission depletion (STED) laser pulses are integrated in a graphical user interface (GUI).
Increases the local contrast of an image. CLAHE uses the contrast limited adaptive histogram equalization to process. The contrast amplification in the vicinity of a given pixel value is delivered by the slope of the transformation function. This ImageJ plugin has three main parameters: block size, histogram and max slope.
Determines the focal plane by using the contrast around a given pixel. MaxContrastProjection contains functions to perform various other types of projections, including a maximum intensity projection. It calculates the local contrast of an input image for every pixel of the image over a given window centered on that pixel.
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.
Serves for correcting the intensity decay due to the photobleaching. Bleach Correction is an ImageJ plugin that works with either 2D or 3D time series. It also contains features to proceed to bleach correction. This tool is composed of three different methods: (1) the simple ratio method, (2) the exponential fitting method and (3) the histogram matching method.
Corrects image defects caused by uneven illumination in fluorescent microscopy. Background Correction is an ImageJ plugin that can realize several tasks: (1) it generates a background image estimated through iterations of the minimum ranking with the number of iterations defined by the user; (2) it subtracts the background image from the original image; and (3) it generates a result image.
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