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.
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.
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.
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.
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.
Estimates the positions and spacing between sections (or at local points) of three dimensional image data. Z-Spacing is an image-based method for the correction of continuous and discontinuous non-planar axial distortions in serial section microscopy. It may be applied to any imaging modality that acquires 3-dimensional data as a stack of 2-dimensional sections. It also provides plugins for both Fiji and TrakEM2.
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.
Provides a toolbox for neuropil decontamination in calcium imaging datasets. FISSA removes several sources of contamination without leading to negative signal artefacts by presenting a standardized and user-independent method. This software process by determining a set of neuropil regions around pre-defined somatic regions of interests (ROI). It utilizes non-negative matrix factorization nuclear magnetic resonance (NMR) to split the signals form these regions.
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.
Allows users to automatically count mitotic cells, neurons and glia. DeadEasy caspase is a program that identifies cells based on a combination of pixel intensity and minimum volume in 3D. This tool is designed as an ImageJ plug-in and can be used for analyzing cell survival and cell death in development and in disease, such as neurodegenerative diseases and ageing.
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.
Assists users to count automatically the number of mitotic cells labelled with anti-phospho-histone H3 and of glial cells labelled with anti-Repo in Drosophila embryos. DeadEasy Mito-Glia is a program that can quantify cells labelled with other nuclear markers. It can be used to compare cell counts between large samples of wild-type and mutant specimens, to infer gene function.
Allows analysis of a range of parameters measured in 3D cell culture based on 2D images. PCaAnalyser is an automated image-analysis based software developed as an ImageJ plugin. The software enables high-throughput analysis of images acquired from cells grown in a 3D matrix. It is able to reproducibly analyze immuno-staining of different markers known to be involved in cancer progression including CXCR4, α6 and β1 integrin subunits.
Provides solutions to users for viewing, modeling, and analyzing 3-D image data for structural biology. IMOD is designed for observing data from tomographic, serial section, and optical section reconstructions. Moreover, this program is also able to measure areas, volumes, and contour lengths, and to count objects of any model class.
Allows users to detect and count fluorescent signals in microscopy images of cells. Blob Finder is a free software that performs two types of analysis: (i) an average count, for quantifying the number of nuclei and signals in an image; (ii) and a single cell analysis, that assigns each signal to the closest cell and get a signal count for each cell in the image. It also performs on-z_stacks of the cell with a maximum projection to project the image data into a 2D image.
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.
Allows users to implement and assemble control software for custom-built microscope systems. Helio provides a framework, built around a collection of components arrangeable according user needs, which can support multiple hardware and functional combinations. The application is able to handle a wide range of laser-scanning including galvanometric scan mirrors or resonant scanners as well as camera images.
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.
A 4-D image processing platform for the work with laser scanning and wide field microscopes. TIKAL provides a registration software for correcting global movements and local deformations of cells as well as 2-D and 3-D tracking software.
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.
Identifies cells, and produces a stack of images with the same number of images as the original raw stack, where the identified cells are reproduced in corresponding locations. DeadEasy Larval Glia permits users to count automatically glial cells labelled with anti-Repo in the Drosophila larval nervous system (VNC). Moreover, this tool can also be used for any other nuclear markers in larval tissues so long as the nuclei are not too close together.
Allows users to perform phase correlation registration to correct movement that occurs as a result of sample drift in three-dimensional (3D) time lapse experiments. Correct 3D Drift is a Fiji plug-in assisting in the correction of the sample drift. It compensates for sample translation or alterations in focal position by utilizing phase correlation to register each time-point of a four dimensional (4D) confocal datasets.
Aims to analyze the dynamics of macromolecular assemblies with high spatial and temporal resolution. QFSM allows users to study spatial and temporal relations between the formation, turnover, and mechanical outputs of the filament network. It assists in identifying and tracking speckles and utilizes their location, appearance, and disappearance to derive network flows and assembly/disassembly maps.
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.
Offers a platform for neurons rebuilding. NeuRA is able to handle image stacks from 2-photon microscopy and to perform their automatic conversion. The application includes a graphic interface allowing users to filter raw data for then segmenting it. Lastly, the software can reconstruct the geometry. It can be used for investigating neuronal plasticity.
Provides a high-throughput image processing workflow designed for reducing hands-on analysis time confocal, epi-fluorescence, and two-photon microscopy images. Chrysalis can automate image processing steps. This method identifies subtle differences in cell phenotype and cell-cell interactions, while also offering significant reduction in hands-on analysis time. It can be applied to a broad range of biological questions.
Allows users to count the number of neurons stained with antiHB9 antibodies in Drosophila embryos. DeadEasy neurons is an image processing and object recognition method that detects neuronal nuclei labeled with HB9 over background from a stack of confocal images. Moreover, this tool is designed to automatically count the neurons in 3D.
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.
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.
Measures the optical field and the intensity distribution of the illumination light in a confocal microscope under several imaging conditions. PSF Lab is built on a vectorial model that takes account of various parameters such as light polarization, high numerical aperture objectives, effects of immersion medium, sample medium and coverslip. It calculates 2D section of point spread function (PSF) and full 3D PSF can be obtained via stack of several calculations.
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.
It is the ideal "glue" for easily integrating dissimilar fluorescent microscope hardware and peripherals into a single custom workstation, while providing all the tools needed to perform meaningful analysis of acquired images. The software offers many user-friendly application modules for biology-specific analysis such as cell signaling, cell counting, and protein expression.
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).
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.
Allows combined image and analogue signal acquisition and analysis. WinFluor is a program that enables users to simultaneously collect cell fluorescence image, patch clamp current and voltage signals. The software includes several features such as detection and analysis of event waveforms, display of excitation spectra, averaging of images or stimulus pulse generation.
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.
Serves for iterative image deblurring. PID allows users to deconvolve a color image by splitting the channels and deblur each channel separately. It contains a graphical user interface (GUI) permitting users to specify several types of details such as stopping tolerance, threshold, or log convergence.
Aims to correct clarification of illuminated background. Rolling Ball Background Substraction determines a local background value for every pixel by averaging over a large ball around the pixel. This value is hereafter subtracted from the original image.
Segments and studies stacks of image data. Costanza can be very useful for data from fluorescent microscopy. Its aim is the segmentation of nuclei marked cells in three dimensions. This tool returns the result both as cells/intensities marked in images. It employs intensity thresholds that allows for segmentation of data of varying intensity. This module gives to users 3D median filter as an optional noise reduction processor.
A version of the public domain image analysis software NIH Image that has been extended to handle the loading, display and analysis of scanning microscope images. Image SXM supports SAM, SCM, SEM, SFM, SLM, SNOM, SPM and STM images.
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.
Permits users to remove a non-uniform background. Nonuniform Background removal can find a least-squares fit of background samples within the image to one of two intensity profiles: a plane, or a 2D cubic polynomial. It can perform on either the current image in a stack or on an entire stack. The software operates in conjunction with the region-of-interest manager, defined by users.
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.
Manages instrument control, image processing and data analysis. SlideBook can drive hundreds of devices including microscopes, stages, lasers, wheels, piezos, scanners or shutters. It acquires data in 3D format over time, color, and specimen locations in customizable experiment protocols. This tool offers a solution to investigate images and obtain statistical data via a wide variety of algorithms while maintaining original data integrity.
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