Find and compare the best bioinformatics software tools for tracking particles on dynamic images acquired by conventional fluorescence microscopy. Tools are ranked by the biomedical research community.
Consists of a tracking Matlab software. u-track is a program designed to perform several actions: (1) track dense particle fields, (2) close gaps in particle trajectories resulting from detection failure, and (3) capture particle merging and splitting events resulting from occlusion or genuine aggregation and dissociation events. Its core is based on formulating correspondence problems as linear assignment problems and searching for a globally optimal solution.
A Matlab software developed for the purpose of proving the principle that full microtubule dynamics can be tracked and inferred based on +TIP marker live cell image sequences only. Note, this package will not be maintained and it is not set up as a user-friendly software.
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.
A free, open-source system designed for flexible, high-throughput cell image analysis. CellProfiler can address a variety of biological questions quantitatively, including standard assays (for example, cell count, size, per-cell protein levels) and complex morphological assays (for example, cell/organelle shape or subcellular patterns of DNA or protein staining).
Correlates local cortical fluorescence with membrane movement. Quimp is based on the electrostatic contour migration method (ECMM) that consists of an improvement of a boundary tracking approach. It reduces sum of path lengths connecting all pairs of points, equivalent to minimizing the energy required for cell deformation. This tool is useful to study time series of several hundreds of cells per experimental condition.
Analyzes and detects cell migration and morphodynamics. ADAPT permits rapid whole-cell analysis of time-lapse videos, providing data on cell morphology, membrane velocity, and temporal changes in any fluorescent protein of interest at the cell periphery. It allows the tracking of cell migration and the automated detection of individual membrane protrusions, outputting data on local membrane velocity, change in protrusion size, and local recruitment of proteins to the cell membrane.
Enables cell lineage tracking. MicrobeTracker utilizes cell shape and timelapse information to achieve cell outlining. It can track fluorescently labeled molecules in cell lineages over several generations or in difficult-to-resolve samples, such as densely-packed or filamentous cells, from time-lapse sequences. This tool is delivered with an accessory tool, called SpotFinder, that detects small round spots, generating precise cell coordinates of fluorescently labeled foci inside cells.
Allows spatial point pattern and interaction analysis. MosaicIA provides standardized ways to (1) correct for the influence of the distribution of points within one set onto the distance distribution to another set; (2) infer parameters of the interaction potential, such as the strength and length scale of the interaction; (3) perform statistical hypothesis tests for the presence of an interaction. It has been tested on both synthetic and real-world data.
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.
A simple, user-friendly tool for interactive image classification, segmentation and analysis. It is built as a modular software framework, which currently has workflows for automated (supervised) pixel- and object-level classification, automated and semi-automated object tracking, semi-automated segmentation and object counting without detection. Most analysis operations are performed lazily, which enables targeted interactive processing of data subvolumes, followed by complete volume analysis in offline batch mode.
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.
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.
Provides all the tools you need to visualize, analyze and validate 3D fluorescence images from a wide range of confocal microscopy, widefield and high content screening systems and is fully integrated for a seamless user experience. Get a full picture of the biological process with rapid, interactive, high-resolution volume rendering of time resolved, multichannel 3D data sets using Volocity software.
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.
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.