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.
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.
Designed to extend any base neuron-tracing algorithm to be able to trace virtually unlimited data volumes. UltraTracer was applied to neuron-tracing algorithms with different design principles and tested on challenging human and mouse neuron datasets that have hundreds of billions of voxels. Results indicate that UltraTracer is scalable, accurate, and about 3 to 6 times more efficient compared to other state-of-the-art approaches.
Explores and annotates large-scale volume data. KNOSSOS is a standalone software that allows user to screen neurites by using three orthogonal views and is able to handle data from serial blockface scanning electron microscopy (SBFSEM). The application provides both a skeletonization and a 3D segmentation mode. The software can also be customized by Python plug-ins as well as be incorporated into external workflows.
Allows to implement NBLAST neuron similarity algorithm. Nat.nblast is an extension of the “nat” software, and supplies a collection of NBLAST-related functions. It executes search of databases for neurons, and permits to compare groups of neurons. A distance matrix for hierarchical clustering can be produced by this tool.
An open source application for the visualization and analysis of 4D biological datasets. Developed by researchers, it is primarily used for the analysis and quantification of 4D live-imaged confocal data. The software's modular design makes it easy to include existing libraries, or to implement new algorithms. Cell geometries extracted with MorphoGraphX can be exported and used as templates for simulation models, providing a powerful platform to investigate the interactions between shape, genes and growth.
An algorithm for automated three-dimensional shape analysis from laser scanning microscopy images. The Rayburst algorithm provides a primitive for the development of higher level algorithms that solve specific shape analysis problems. Examples are provided of applications to 3D neuronal morphometry: (i) estimation of diameters in tubular neuronal dendritic branching structures, and (ii) measurement of volumes and surface areas for dendritic spines and spatially complex histopathologic structures.
A freely available software tool for the quantitative characterization of neuronal morphology. L-Measure computes a large number of neuroanatomical parameters from 3D digital reconstruction files starting from and combining a set of core metrics.
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.
Allows reconstruction of neuronal structures from confocal and multi-photon images. NeuronStudio provides tools for manual, semi-manual, and automatic tracing of the dendritic arbor as well as manual and automatic detection and classification of dendritic spines. In addition, advanced 2D and 3D visualization techniques facilitate the verification of the reconstruction, as well as allowing accurate manual editing.
Allows users to create subject-specific musculoskeletal models for the OpenSim software. nmsBuilder is a web application dedicated to the modelization of biomedical data. The platform provides a graphical user interface that allows users to handle user-defined files for visualizing, merging and setting various parameters to finally generate and export musculoskeletal models.
An application for semi-automated tracing of neurons to quickly annotate noisy datasets and construct complex neuronal topologies. Simple Neurite Tracer is designed to allow easy semi-automatic tracing of neurons or other tube-like structures (e.g. blood vessels) through 3D image stacks. The plugin has built-in tools for analysis and hardware accelerated 3D visualization of the results. Data can be imported and exported in SWC files for interaction with other software, or details of the traces can be exported as CSV files for analysis in spreadsheets or statistical software. The native file format is open and XML-based.
An easy-to-use, open-source software package for tracking kinetochores from live-cell fluorescent movies. KiT supports 2D, 3D and multi-colour movies, quantification of fluorescence, integrated deconvolution, parallel execution and multiple algorithms for particle localization. KiT includes a user-friendly GUI (Graphical User Interface) for selecting ROIs (Regions Of Interest; to select cells and exclude spurious background fluorescence), parameter configuration and execution of KiT. Tracking may be executed from within the GUI or later. The GUI allows selection of particle detection algorithms per channel and modification of the most commonly used options. KiT also includes a GUI for post-tracking processing, enabling basic diagnostics and track quantification, such as kinetochore speeds and autocorrelation. The GUI collates data from each tracked ROI and saves a .mat file for later user-specific processing.
A software for 3D neuron tracing. APP2 prunes an initial reconstruction tree of a neuron’s morphology using a long-segment-first hierarchical procedure instead of the original termini-first-search process in APP. This method allows users to trace large images. APP2 was bench-tested on 700 3D microscopic images and it was found that APP2 can generate more satisfactory results in most cases than several previous methods. This software has been implemented as an open-source Vaa3D plugin.
A modular software tool for efficient quantification of biological tissues based on volume data obtained by biomedical image modalities. TiQuant includes a number of versatile image and volume processing chains tailored to the analysis of different tissue types which have been experimentally verified. It implements a novel method for the reconstruction of three-dimensional surfaces of biological systems, data that often cannot be obtained experimentally but which is of utmost importance for tissue modelling in systems biology.
An interactive 3D axon tracking and labeling tool to obtain quantitative information by reconstruction of the axonal structures in the entire innervation field. AxonTracker-3D has been developed to facilitate the connectome function analysis in large-scale quantitative neurobiology studies. It can display the three orthogonal views of the current location of the centerline along with a visualization of the tracking results. The workflow consists of three steps: (i) re-slice the axon tubes along its orientation; (ii) extract 2D and 3D features from the slices and spheres rounding the center points; (iii) select samples to train AdaBoost classifier. Questions such as whether the spatial distribution of the axons are random in nature or follow a certain pattern can be answered with this tool.
Identifies neuronal soma in large-scale images obtained with confocal light sheet microscopy (CLSM). Brain cell finder provides three methods: a mean shift clustering, a supervised semantic deconvolution by means of neural networks and a manifold learning. It enables the detection of soma centers, image enhancement and filtering false positives (FPs). This tool was used to build a map of Purkinje cells in the whole mouse cerebellum.
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.
A robust approach to reconstruct 2D and 3D (non-)biological spatial networks from gray-scale image data. By constructing weighted networks and computing their seminal network properties, img2net allows an extensive quantification and statistical comparison of network topologies. img2net can be readily used for analyzing image data of arbitrary 2D and 3D network-like structures.
A statistical method for tracing the branch centerlines of neurons based on Bayesian multi-object tracking using probability hypothesis density (PHD) filtering. hgpush is able to simultaneously trace out multiple neuron structures in a probabilistic fashion so that the same neuron segments may be covered multiple times and are thus supported by more evidence. The main novelty is that it combines the problems of neuron segment detection and linking into one framework by performing simultaneous multi-object tracking. hgpush solves the computational problems of direct Bayesian multi-object tracking and allows convenient handling of bifurcations and terminations during the tracing process by modeling of spawned objects and observation clutter.
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.
Detects central regions for both dendrites and spines using gradient vector tracking and feature point discovery. This method was developed for segmentation in 3D confocal microscopy images of medium-sized spiny neurons (MSNs). This method is able to effectively find objects with variational shapes and sizes. It can also be used for other applications of object recognition and segmentation because it is fully automated and requires no user interaction.
An interactive Qt4 analysis tool for attaching the intrinsic root coordinate system to 3-D confocal recordings of the Arabidopsis root apical meristem. This allows quantitative comparative studies of root populations in a sound and intuitive context. iRoCS Toolbox consists of the data browser labelling and a set of command line tools for batch processing. Main features are: (i) 3-D Visualization of the volume in an orthographic view; (ii) manual annotation of anatomical reference structures (QC, nuclei); (iii) automatic detection and annotation of cells and/or nuclei with several meaningful properties, like position, radius, tissue, cell file, cell cycle state, volume; (iv) full control. Any step can be manually corrected and re-fed into the modeling; (v) retrieval and localization of key events like cell divisions.
Annotates and screens 3D image data with the aim of easing circuit rebuilding. PyKNOSSOS is a standalone software which provides four working modes: (i) browsing files including a for multi-resolution viewing, (ii) a tracing features that is able to perform manual skeleton tracing, orthogonal tracing and arbitrary reslices; (iii) a tagging module; and (iv) synapse annotation tools. In addition, it includes a feature for visualization by using VTK-Python bindings.
A plugin for bone image analysis in ImageJ. BoneJ provides free, open source tools for trabecular geometry and whole bone shape analysis. It calculates several trabecular, cross-sectional and particulate parameters in a convenient format. Java technology allows BoneJ to run on commodity computers, independent of scanner devices, fully utilising hardware resources. ImageJ’s plugin infrastructure provides a flexible working environment that can be tailored to diverse experimental setups. BoneJ is a working program and a starting point for further development, which will be directed by users’ requests and the emergence of new techniques.
Provides specific issue of 3D distance analysis. Corsen is an application that quantifies mRNA to mitochondria distances and analyzes the corresponding cell distribution. It also offers semi-automated digital image acquisition coupled with automated image analysis that can be conducted on a large cell population. This method can reveal subpopulation features that are masked in population averages and cannot be detected by human eye analyses.
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.
A software application on MATLAB to visualize surface data from 3D fluorescence microscopy. Map3-2D accurately accurately projects up to five-dimensional (5D) fluorescence microscopy image data onto full-content 2D maps. Similar to the Earth's projection onto cartographic maps, Map3-2D unfolds surface information from a stack of images onto a single, structurally interconnected map. By cross-referencing between the 2D map and the original image stack, precise quantitative analyses of intensities and shapes are easily and intuitively executable.
Provides all the necessary methods for nuclei segmentation, cell identification and analysis of cell interaction in 3D. 3D Tissue Organization Toolbox is an ImageJ plugin that covers different aspects of spatial analysis of tissues in 3D, ranging from nuclei segmentation to analysis of different aspects of cellular interaction and network mapping. It was used to investigate current and novel aspects of the unique architecture of the pancreatic islet of Langerhans.
Automates neuron reconstruction machine integrating online image analysis with automated multiphoton imaging. SmartScope2 takes advantage of a neuron’s sparse morphology to improve imaging speed and reduce image data stored, transferred and analyzed. It is able to produce the complex 3D morphology of human and mouse cortical neurons with six-fold reduction in image data requirements and three times the imaging speed compared to conventional methods.
Serves for the high-throughput analysis of root system architecture. GiA Roots estimates root system architecture (RSA) traits from a large number of root system images and identify roots from the background, i.e., segmenting the image. It includes: an optional userassisted processing of images, scale calibration, trait selection, image segmentation, and trait measurement.
An open source system for three dimensional digital tracing of neurites. Neuromantic reconstructions are comparable in quality to those of existing commercial and freeware systems while balancing speed and accuracy of manual reconstruction.
Provides assistance for distance analysis and object-based 3D co-localization. DiAna incorporates two 3D procedures for image segmentation and 3D automated object-based co-localization in-depth analysis. It measures the distribution of distances between objects in 3D. This software allows users to label images and provides features tools for the segmentation of the objects and extended functionalities for 3D distance analysis and 3D measurements.
Builds 3D neural meshes. Neuronize is a set of methods designed taking the morphological information extracted through computer-aided tracing applications as the starting point. The software generates 3D models for neuronal cells that approximate the cell membrane at different resolution levels, allowing balance to be reached between the complexity and the quality of the final model. The software is conceived to overcome the problems caused by the unrealistic somata and low quality unconnected 3D mesh.
A broadly applicable algorithm and a comprehensive open-source software implementation for automated tracing of neuronal structures in 3-D microscopy images. Open Snake Tracing System has been integrated to the Farsight toolkit. The core 3-D neuron tracing algorithm is based on three-dimensional (3-D) open-curve active Contour (Snake). It is initiated from a set of automatically detected seed points. A suite of pre-processing algorithms enable the system to accommodate diverse neuronal image datasets by reducing them to a common image format. These algorithms form the basis for a comprehensive, scalable, and efficient software system developed for confocal or brightfield images. It provides multiple automated tracing modes. The user can optionally interact with the tracing system using multiple view visualization, and exercise full control to ensure a high quality reconstruction.
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.
Allows users to reconstruct and proofread neuronal morphologies in light microscopy images. The system incorporates automatic tracing and manual editing of neuron reconstruction into a cooperative 3D interactive visualization-assisted environment, which is a powerful tool for analysis of complex neuronal images.
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.
It is an organized collection of software modules for image data handling, pre-processing, segmentation, inspection and editing, post-processing, and secondary analysis. These modules can be scripted to accomplish a variety of automated image analysis tasks.
An automated algorithm for 3D cell nuclei segmentation based on gradient flow tracking. The proposed algorithm is able to segment closely juxtaposed or touching cell nuclei obtained from 3D microscopy imaging with reasonable accuracy. To validate the efficacy and performance of the proposed segmentation algorithm, we evaluated it by using synthesized and real biological images. The results show that the algorithm is able to segment juxtaposed nuclei correctly, a persistent problem in the field of cellular image analysis.
It is able to apply pattern recognition algorithms to two- and three-dimensional biological image sets as well as regions of interest (ROIs) in individual images for automatic classification and annotation. The customizability of BIOCAT is expected to be useful for providing effective and efficient solutions for a variety of biological problems involving image classification and annotation.
An automatic neuron tracing method. DF-Tracing can automatically trace complicated neuron structures set in noise-contaminated microscopic images. This method first extracts the neurite signal (foreground) from a noisy image by using anisotropic filtering and automated thresholding. Then, DF-Tracing executes a coupled distance-field (DF) algorithm on the extracted foreground neurite signal and reconstructs the neuron morphology automatically.
Measures accurately cell membrane lipid packing without cytosolic contributions using a single dye. The Spectral Imaging Toolbox was designed for spectral analysis of high magnification images of single or sub-confluent cells, vesicles and microbubbles. This method permits to process and analyze a dataset containing over 1500 cells in a few hours. It also addresses a growing need to process large spectral imaging datasets and data from experiments with multiple exposures.
Allows to visualize confocal microscopy data. FluoRender can preserve original fluorescence intensity values on graphics hardware and supports far more than three Red-Green-Blue (RGB) channels. It permits to proceed analysis of many channels of volume data from mutant-control scans and to construct anatomical atlases. The tool allows to visualize simultaneously 96 independent channels without convertion into RGB channels or pseudosurfaces.
Allows users to estimate Germinal Center (GC) volumes from standard multidimensional image data. pyBioImage is a cross-platform bioimaging application which supports several data formats and provides a way for visualization and analysis. The application includes a module: ExtractGC, based on a pseudo-recursive segmentation algorithm, which allows users to visualize the GC volumes in 3D while providing GC size and volume statistics.
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.
Allows automatic reconstruction of entire tissue blocks. AnalyzeSkeleton calculates the optimum transformation at each pyramid level. It is able to store cellular-level phenotypic information. The tool (1) acquires images, (2) automatically and rigidly registers them, (3) segments the structures of interest, (4) groups their resulting contours, (5) locally or elastically refines registration, and (6) reconstructs structure in 3D based on the grouped contours.
A software tool for reconstructing neurons from fluorescence microscope images. The main function of neuTube is to generate a neuron structure from a 3D image with user interaction, which mainly consists of mouse clicks. neuTube can also load SWC files from any other source for visualization or further editing.
Analyses raw confocal microscopy images. Analyses options include the whole image, specific regions of the image (cropping) and z-axis analysis of the same image. Batch analysis of a series of images with identical criteria is also one of the options. There is no need to either re-orientate any specimen to the horizontal or to do a thresholding of the image to perform analysis. TTorg includes a synthetic "myocyte-like" image generator to test the plugin's efficiency in user's own experimental conditions. This plugin was validated on synthetic images for different simulated cell characteristics and acquisition parameters.