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.
Analyzes biomedical images acquired by various types of microscopes. MiToBo completely separates the implementation of image processing algorithms from potential user interfaces. MiToBo provides a framework for implementing image analysis algorithms allowing for automatic documentation and automatic user interface generation, and includes the graphical programming editor Grappa for user-friendly design of more complex processing pipelines.
Provides an automated and qualitative visualization of time-lapse microscopy data. SeeVis automatically preprocesses movie frames, finds particles and traces their trajectories. It then permits users to visualize them in a space-time cube offering three different color mappings to highlight different features. It also supports the user in developing a mental model for the data.
Provides assistance for visualization and analysis of multi-modal, multi-process and time-lapse microscopy morphological and functional images at single-cell level. SCIP can execute an automatic or manually corrected segmentation of cells and lineages, automatic alignment of different microscopy channels and identify, measure and determine fluorescent spots. This software aims to ease the finding of relationships between cellular processes from small-scale to large-scale in single cells and cell lineages.
An open source, platform-independent viewer making use of the latest web technologies that allows seamless access to images and associated metadata for each image. HTML5 PivotViewer provides a powerful method to allow end users to mine their data.
Provides users libraries and command line tools for the processing and analysis medical images. MIA is a general purpose image processing toolbox that puts its focus on gray scale image processing. This resource provides libraries that can be used to shape newly created algorithms into new command line tools. Various image processing algorithms are also implemented, amongst these specific segmentation algorithms, a variety of image filters and combiners, and generic image registration algorithms.
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 medical image computing and visualization. 3D Slicer is an open source software platform which offers a wide range of features for versatile visualization, exploration and quantitative analysis of imaging data. It enables fusion of functional and anatomical data and provides a variety of generic and specialized tools for their processing and multimodal analysis. The software allows exploration of the imaging datasets in two, three and four dimensions.
Automates analysis of neuronal morphologies in immuno-fluorescence images. SynD intends to assist users in quantifying dendrite and synapse characteristics. The application performs successively the detection of soma, neurites, and synapses. It can be used to enable the simultaneous analysis of multiple morphological features and permits the screening of genetic and pharmacological treatments.
Allows users to perform image analysis, optimized for measurement of time-lapse microscopy images. CellTool is designed for parallel computing and contains tools for image processing, data management, graphical data presentation and mathematical modeling. It permits researchers to track and measure objects of interest and to display or modify data.
Enhances KNIME by providing algorithms and data structures to process and analyse images. The KNIME Image Processing Extension uses and integrates state-of-the-art libraries such as ImageJ1 and ImageJ2, SCIFIO, OMERO, ClearVolume, ImgLib2, CellProfiler, TrackMate and others. It enables users to explore images and labeling in more detail. It also offers a range of general (pre-)processing techniques to enhance image quality.
Discovers the “classical” endpoints neuron quantification and neuronal morphology but also novel endpoints like radial migration and neuronal density distributions within the Neurosphere Assay. Omnisphero aims to automated high-content image analysis (HCA) developmental neurotoxicity (DNT) screenings. It can be applied in other 3D in vitro systems such as in the migration assay of tumor spheroids.
An intuitive and qualitative visualization technique that can reveal the presence of various flow structures in experimental videos. Flowtrace can be used either as a primary analysis tool for presence/absence studies or to motivate the use of more complicated flow quantification techniques. This technique is based purely on image processing of the input data, rather than numerical reconstruction of scalar fields like vorticity, allowing it to be used as a straightforward “first pass” characterization technique for biological systems where traditional techniques are either unnecessary to support qualitative observations, or prohibitively difficult due to the length and timescales involved. Flowtrace algorithm is implemented as an open-source package for MATLAB, Python or ImageJ.
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.
Permits users to conduct 3D modeling, image processing and measurement magnetic resonance imaging (MRI), computed tomography (CT), positron-emission tomography (PET), microscopy, scientific, and industrial imaging. 3D-DOCTOR constructs 3D surface models and volume rendering from 2D cross-section images in real time. It enables the alignment of misaligned slices in an automatic or semi-automatic manner with image alignment functions.
Assists users to explore, process and analyze images or movies. ImageA is a program that offers researchers several functionalities to perform about images, among other things: display and exploration, texture analysis, geometrical transformation, images transformation, two dimensional filters, measure tools, image editing, or import and export.
Consists of a data analysis and visualization application. ParaView provides qualitative and quantitative techniques to build visualizations allowing the investigation of data. It gathers an interactive 3D interface and a programmatical interface. This tool can be applied to large datasets with distributed memory computing resources. It is useful for datasets of petascale size as well as for smaller data.
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.
Offers read-only access to the information contained in files in CZI format. libCZI provides several functionalities such as: (1) reading subblocks and get the content as a bitmap; (2) reading subblocks which are compressed with JPEG-XR; (3) works with tiled images and pyramid images; (4) composing multi-channel images with tinting and applying a gradation curve; and (5) giving access to metadata.
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