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.
Allows the detection of cells, the creation of seeds and boundaries for the automatic segmentation of cell geometries. Balloon Segmentation is an algorithm implemented as a Java ImageJ plugin assisting users in the analysis of images. It enables the measurement of cellular properties in intact tissue while retaining the cellular context for subsequent studies.
Consists of a cloud based deep learning solution for image segmentation of light, electron and X-ray microscopy. CDeep3M serves for image segmentation tasks of large and complex 2D and 3D microscopy datasets by taking advantage of the underlying architecture of a deep learning convolutional neural network (CNN) called DeepEM3D. This software is also available on the Amazon Web Services (AWS) platform.
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.
A tool for segmentation, fluorescence quantification, and tracking of cells on microscopy images. CellX decodes the information across the cell membrane and guarantees optimal detection of the cell boundaries on a per-cell basis. Graph cuts account for the information of the cell boundaries through directional cross-correlations, and they automatically incorporate spatial constraints. The method accurately segments images of various cell types grown in dense cultures that are acquired with different microscopy techniques.
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.
Allows analysis of epithelial tissues. EpiTools automates image analysis including cell segmentation and cell tracking. It describes dynamic cellular behavior and allows users to study the power of in vivo imaging. This tool supplies a graphical user interface to simplify its utilization by users and for segmenting and tracking the contours of cell membrane signals obtained from 4D confocal imaging. It is intended primarily for biologists with no computer-science background.
Provides general purpose functionality for reading, writing, processing and analysis of images. In the context of microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and use of existing tools in the R environment for signal processing, statistical modeling, machine learning and data visualization. It uses ImageMagick to read and save images, and supports more than 80 image formats, including JPEG, TIFF, TGA, GIF and PNG. EBImage also supports standard geometric transformations such as rotation, reflection, cropping, translation and resizing. Classical image processing tools are available: linear filtering, morphological erosion and dilation, fast distance map computation, contour delineation and area filling.
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.
Consists of a high-throughput single-cell imaging and image processing protocol. TIMING conducts large-scale automated video array investigations. It can construct quantitative analyses of cell interaction behaviors at single-cell resolution with visual confirmation. This tool counts the cells in each nanowell, finds their types based on cell-type markers, and provides measurements of size, location, shape, and movements of cells.
Segments and tracks budding yeast cells. DISCO is a comprehensive framework structured into several stages for integrated identification, segmentation and tracking of cells: (i) identification of physical features of the microfluidic device, (ii) supervised classification to identify cell centers, (iii) segmentation using a morphologically constrained cell-shape model, (iv) incorporation of temporal information to refine cell center prediction and (v) iterative greedy optimization of cell contours.
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.
Assists in analyzing white adipose tissue cellularity in histological sections. Adiposoft automates the analysis of histological adipose tissue samples and requires a single click to analyze a whole set of images. This tool works with standard histological sections, whereas the analysis of cells in suspension requires collagenase digestion of the adipose tissue sample.
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.
Segments touching cells in 2D images. iCut provides an integrative cut algorithm merging information about spatial location and the intervening and concave contours. It aims to facilitate high-throughput analysis of brain anatomy by using massive image datasets and to afford the automatic and precise segmentation of touching cells. It was tested with both simulated and experimental image datasets.
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.
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.
Analyzes protein trafficking in neuronal florescence microscopy videos. DendritePA is an automated pattern recognition software that uses video bioinformatic algorithms to automatically obtain spatiotemporal pattern information on protein dynamics. The program analyzes protein localization in neurons using multi-channel florescence microscopy and relates it to dendritic spine shape and protein activity state.