Processes quantitative analyses of high throughput cell migration assay. WIS-PhagoTracker facilitates morphometric analysis of modified Phagokinetic tracks that are visualized by using a screening microscope. This software applies a multi-scale segmentation algorithm to characterize several morphometric parameters such track area, perimeter, major and minor axis and solidity for each track. It can support single image files and run batch processing of multiple plates.
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.
Performs crowd-based images annotation. Quanti.us is a portal that assists users in recruiting groups of untrained Mechanical Turk workers (Turkers) to annotate images using a set of interaction tools. The platform enables uploading of image sets, selection of an analysis tool, and provides sets of instructions. Users can gather hand annotations by marshaling paid Turkers to annotate a range of image types. Quanti.us thus makes crowd analysis of scientific images applicable to several annotation problems.
Finds dynamic changes in pixel intensity between image frames. MUSCLEMOTION expresses the output as a relative measure of movement during muscle contraction and relaxation. It can be employed for multiparameter recording conditions and experimental settings using transmitted light microscopy, fluorescent membrane labeling, fluorescent beads embedded in soft substrates or patch clamp video recordings.
Allows representation of multidimensional cellular measurements. PhenoPlot is a toolbox that permits visualization of up to 21 variables. It may be useful for determining the morphology of breast cancer cell lines or for understanding and interpreting multidimensional cellular imaging data. To assist users, this tool employs many visual elements such as differently sized, coloured and structured objects. It provides effective and intuitive pictorial representations of cellular phenotypes.
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.
A simple and user-friendly ImageJ plugin dedicated to the characterization of nuclear morphology and chromatin organization in 3D. Starting from image stacks, the nuclear boundary is delimited by combining the Otsu segmentation method with optimization of nuclear sphericity. Chromatin domains are segmented by partitioning the nucleus using a 3D watershed algorithm and by thresholding a contrast measure over the resulting regions. As output, NucleusJ quantifies 15 parameters including shape and size of nuclei as well as intra-nuclear objects and their position within the nucleus.
A framework for the automated determination of neutrophil extracellular traps (NET) content, based on visually annotated images which are used to train a supervised machine-learning method. The final output of NetsDetermination is a single fraction measurement which does not directly relate back to pixel assignments.
Retrieves diverse shortest paths between two end-points. DiversePathsJ returns paths that can then be swiftly browsed and displayed on the image using the arrow keyboard keys, or exported in generic formats for further processing. It allows users to analyze multiple instances of the same objects exhibiting slight variations without the need for fine-tuning of the cost function. This tool is not restricted to quantitative estimation of shape features such as length and bending. It covers every problem in which a path is to be searched between two end-points.
Deduces multi-feature phenotypic crosstalk from perturbation assays. PHOCOS takes into consideration the potential interactions among different attributes of biomarkers. It can retrieve core, direct-effect motifs from missing links, noise and indirect effects. This tool can produce ‘high-resolution’ views of which phenotypic attributes support interaction among biomarkers. It is useful for microscopy images and others biological datasets.
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.
A wavelet-based image-analysis software providing a fast automatic detection scheme for circular patterns (spots), combined with the precise estimation of their size. SpotCaliper is able to automatically find spots of varying size, and gives a precise measurement on their radius. The detections are collected in a table, displaying the following parameters: unique identifier (ID) of the spot, its location (x and y coordinates), radius, confidence, contrast, SNR and type. It is implemented as an ImageJ plugin with a friendly user interface. The user is allowed to edit the results by modifying the measurements (in a semi-automated way), extract data for further analysis. The fine tuning of the detections includes the possibility of adjusting or removing the original detections, as well as adding further spots. The main advantage of the software is its ability to capture the size of spots in a fast and accurate way.
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 users to quantify anatomical traits of rice roots transverse section images. Phiv-Rootcell serves for analyzing several root anatomical parameters based on images of rice root transverse sections. It permits supervised measurements of areas. Moreover, this tool can serve for genetic or physiological studies that investigate root anatomical trait variations.
Measures callose deposits in an automatic way. Callose Measure can recognize particle-like signals thanks to spot detection algorithms. It integrates an edge detection method based on the border tracing approach. This tool is able to conduct sensitive edge-based measurements on size and shape. It can filter out noise signals, split fused fluorescence signals, measure the size/shape of identified callose objects, and recognise patterns of spreading callose.
Offers a platform dedicated to the visualization and investigation of neuronal morphologies. BTMORPH is an open-source library which combines multiples routine to a data structure. This program also leans on a visualization module allowing the representation of neuronal morphologies as 2 and 3 dimensional plots or as dendrogram. It also includes additional wrappers permitting the analysis of multidimensional data in single neurons or the recording of population statistics.
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.
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.
Performs quantitative characterization of muscle phenotypes in time-series images. FMAj is composed of three modules: (i) the first one captures experimental metadata derived from the images or via manual annotation by the user; (ii) the second performs segmentation of muscle cells and nuclei in a semi-automated fashion.; (iii) the third module achieves comparative phenotypic analysis, such as comparing the cell morphology between control and genetically perturbed cells.
A user-friendly image-based classification algorithm inspired by WND-CHARM in (i) its ability to capture a wide variety of morphological aspects of the image, and (ii) the absence of requirement for segmentation. In order to make such an image-based classification method easily accessible to the biological research community, CP-CHARM relies on the widely-used open-source image analysis software CellProfiler for feature extraction.
Assesses the effects of disruption of a given protein on the mitotic spindle. MatQuantify is a standalone software that allows users to identify structural changes in spindle or DNA and can be applied to fluorescence microscopy images for measuring: (i) physical properties, including perimeter, fractal dimension or satellite objects; and (ii) textual properties, such as entropy, intensities and their standard deviation. The application can detect both fine and large-scale changes.
An easy to use software application that will greatly speed and standardize quantification of neuron organization. IPLaminator rapidly analyzes neurite stratification patterns in the retina and other neural tissues. A range of user options allows researchers to bin inner plexiform layer (IPL) stratification based on fixed points, such as the neurites of cholinergic amacrine cells, or to define a number of bins into which the IPL will be divided. Options to analyze tissues such as cortex were also added. Statistical analysis of the output then allows a quantitative value to be assigned to differences in laminar patterning observed in different models, genotypes or across developmental time.
A high throughput method to automatically detect the transition of a cell cluster from two to three cells in thousands of videos. livespin performs a robust implicit tracking of cells even when they are packed, overlap or are not clearly distinguishable. The approach is based on a robust fitting of two-dimensional Gaussian mixture models with two and three components on each frame of the video. livespin is composed of four steps described in this section. The first step consists in localizing the fibronectin patterns and cropping the whole video at those locations to obtain individual cluster sequences, the second step consists in fitting 2- and 3-components Gaussian mixture model (GMM) onto each frame of each video sequence and the third step consists in the identification of the first frame containing three cells (the transition from 2 cells to 3 cells) using the fitting error difference and other features computed from the GMM parameters. The final step consists in the computation of the angle of division in the identified frame.
Automates cell shape extraction in C. elegans embryos. BCOMS provides a user-friendly framework that computerizes not only the segmentation process but also the evaluation process. The performance of BCOMS was validated by comparisons with the ground truth and by comparing the results in two adjacent time points. This method is also applicable to other model organisms by customizing the biological constraints.
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.
Allows determination of the number of foci in a single cell, a focus intensity per cell, as well as a cell intensity. FociCounter was tested by analysing gamma-H2AX foci in CHO and MO59K cells irradiated in vitro with X-rays. It was validated by comparing the results obtained with the outcome of automated image analysis and flow cytometry. The software was developed for research laboratories possessing a fluorescent microscope in combination with a digital camera. FociCounter was designed for the most common image formats that are two-dimensional.
A MATLAB based command line software toolbox providing an automated whole cell segmentation of images showing surface stained cells, acquired by fluorescence microscopy. CellSegm has options for both fully automated and semi-automated cell segmentation. Major algorithmic steps are: (i) smoothing, (ii) Hessian-based ridge enhancement, (iii) marker-controlled watershed segmentation, and (iv) feature-based classification of cell candidates. The command-line interface of CellSegm facilitates scripting of the separate tools, all implemented in MATLAB, offering a high degree of flexibility and tailored workflows for the end-user. The modularity and scripting capabilities of CellSegm enable automated workflows and quantitative analysis of microscopic data, suited for high-throughput image based screening.
Provides high content quantification of muscle features. MyoVision includes fiber number, cross sectional area (CSA), minimum Feret diameter, myonuclear number, and fiber type distribution, without requiring human supervision. It separates connected muscle fibers using the efficient watershed transformation and then fine-tunes the cytoplasmic boundaries using the active contour method. This tool is able to eliminate inter-individual variation.
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.
Allows for quantitative assessment of morphology and pericyte coverage in vascular sprouts developed from human endothelial cells and human pericytes in vitro. Sprout Morphology enables to observe some of the expected effects of anti-angiogenic substances, such as those of vascular endothelial growth factor (VEGF) and platelet-derived growth factor (PDGF) receptor inhibitors. It is a plugin for ImageJ allowing to quantify the results.
Provides an image analysis software for prokaryotes with complex morphologies. BacStalk is an application specialized for automated, label-free, time-resolved image analysis of stalked and non-stalked bacteria. It enables the detection of fluorescence patterns and the morphometric analysis of cell bodies, and their corresponding stalks and buds. It can also visualize fluorescence signals in cells in interactive demographs and kymographs.
Uses deep feature transfer for generating morphological profiles without human interaction. Automating Morphological Profiling with Generic Deep Convolutional Networks achieves higher accuracies than previous classical methods, needs less time and expertise to extract profiles and allows for true automated high content screening by taking the human out of the loop. Furthermore, it enables fully automated processing of microscopy images without need for single cell identification.
Provides an automatic and standardized image segmentation platform. SMASH permits users to measure multiple facets of muscle histology. It carries a high monetary cost and is not specifically designed for skeletal muscle analysis. This tool generates results validated against legacy methods showing largely consistent results between methods for fiber type and centrally nucleated fiber (CNF) percentages. It reduces the border region between adjacent fibers, it is also capable of delineating interstitial space between adjacent fibers when there is an appreciable separation.
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.
A tool for creating and analyzing realistic, meaningful, and quantifiable neuron reconstructions from microscope images. Perform detailed morphometric analysis of neurons, such as quantifying: 1) the number of dendrites, axons, nodes, synapses, and spines, 2) the length, width, and volume of dendrites and axons, 3) the area and volume of the soma and 4) the complexity and extension of neurons.
Marks and links results in a non-destructive way. ObjectJ uses vector objects to display points and paths that non-destructively mark images via a transparent layer. This ImageJ plugin stores the graphical objects into a separate project file. A back-and-forth navigation between results and images is available and the results table can incorporate statistics, sorting, color coding, qualifying and macro access.
Analyzes and measures digital images. Bersoft Image Measurement executes automatically measurements or area, radius and length. It uses vectorial layers to draw the different measurements available. Spatial calibration is provided, and can process Elisa and Western Blot arrays. This tool is compatible with several popular image formats.
Provides assistance for the analysis of high-throughput microscopy-based screens. imageHTS main features are segmentation of cells, extraction of quantitative cell features, prediction of cell types and visualization of data through web interface. This software offers a standardized access to remote screen data to facilitate the dissemination of high-throughput microscopy-based screens.
Provides macros for ImageJ to automatically analyze the size and intensity of objects/regions in microscope images. imagej-interactive-thresholding is useful for the quantification of image data in cell biology and other areas of research. It can measure the fluorescence intensity within the segmented regions in a different image channel. This tool allows users to modify the automatically detected regions prior.
Allows to detect spots in different conditions. Spot Detector can find spots in noisy images 2D/3D; detect nucleus or cell depending on objective; detect spot in specific band/channel; create automatically region of interests (ROIs) from one band and count in the same or an other band; and display detections and tags from image.
Executes automated batch analysis of JPEG images of aniline-blue stained callose deposits. AutoSPOTs identifies and quantifies fluorescent spots on JPEG files. Users can configure filter settings for average sensitivity and accuracy in enumeration of callose deposits. This software offers features such as color filtering, multiple pixels selecting, values recording or average measuring.
Allows to visualize and present your images in several dimensions. The functionality of this imaging toolbox expands constantly with a wide range of different modules that are tailored to specific applications or microscope accessories. AxioVision offers countless functions for applications in the field of biological and medical routine research.
Assists users in stomata detection. Stomatameasurer is an application that uses TIFF fluorescence images of leaves. All analyses are realized in a single step, and the tool prints out some meta information on the files, including treatment, well coords, time, pixel info and stack. A function is included to always gets the stomata objects anyway on the picture.
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.
Permits scientific evaluation of 2D images. GSA Image Analyser is a program that allows (1) automatic surface calculation of the surfaces of all recognized objects, (2) direct length calculation of very complex and very ramified objects, and (3) object counting with an automatic count-function, a grid-intersection-count-function and two manual count-procedures.
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.
Allows users to determine Fourier descriptors and the curvature starting from a closed curve. Fourier Shape analysis is a module that can be run through the ImageJ software. The application consists of three main features allowing the computation of Fourier descriptors, the generation of elliptic Fourier descriptors including a normalized set of coefficients such as rotation or scale invariant, as well as the calculation of curvature.
Calculates standard bone histomorphometry parameters on a digitized trabecular-bone surface, according to the parallel plates model. Map_BoneMicrostructure is an ImageJ plugin for calculating bone area fraction (BA/TA), trabecular thickness (TbTh), trabecular separation (TbSp) and trabecular number per length unit (TbN). The software processes 8-bit grayscale images with black-colored bone-trabeculae on white background.
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