Cell motility is a critical part of many important biological processes. Automated and sensitive cell tracking is essential to cell motility studies where the tracking results can be used for diagnostic or curative decisions and where mathematical models can be developed to deepen our understanding of the mechanisms underlying cell motility.
Allows quantification of cellular and molecular properties and single-cell tracking in time-lapse imaging data. tTt assists users in realization of manual cell tracking and includes possibility to correct, inspect and import existing tracked trees. The application includes tTtConverter, a tool to convert arbitrary time-lapse imaging experiment data formats into the structure required to open them with tTt and qTfy.
A computational framework to annotate complex cellular dynamics. A machine-learning method that combines state-of-the-art classification with hidden Markov modeling for annotation of the progression through morphologically distinct biological states was developed. CellCognition is published as open source software, enabling live-cell imaging-based screening with assays that directly score cellular dynamics.
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.
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.
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.
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.
Allows users to understand the creation of tissue dynamics by cellular processes. TissueMiner enables biologists and physicists to quantify cell state properties and cell dynamics. It simplifies the comparison of quantities within and between tissues. This tool can generate segmented images, referred to as segmentation masks informing users about cell geometry, cell neighbor topology and cell ancestry.
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.
Allows exploration, analysis and interpretation of single-cell data. Vizardous’ core functionality is to visualize time-resolved, single-cell and population data. It can be used for the automated analysis of data as well. With Vizardous, lineage tree drawings can be upgraded with various, time-resolved cellular characteristics. Associated statistical moments link single cell and the population-average level.
Studies cell movement by adopting deep reinforcement learning approaches within an agent-based modeling framework. drl4cellmovement captures the main aspects of cell movement and provides an idea that represents cell behaviors with neural networks trained by deep reinforcement. The software can learn a cell’s optimal path under certain regulatory mechanisms, and can thus examine hypotheses by comparing the similarities between the simulation cell migration paths and the observation data. It was tested through two representative scenarios during C. elegans embryogenesis.
Allows to track populations of neurons with single neuron resolution in the brain of a freely moving C. elegans undergoing large motion and deformation. NeRVEclustering uses non-rigid point-set registration in order to match each segmented neuron in each volume with a set of reference volumes taken from throughout the recording. This tool primarily serves for tracking neurons in brains undergoing large deformations.
Aids users to quantify tumor spheroid dynamics. TASI is a program that allows investigators to: segment spheroid images, extract features describing their shape, growth, and perform mathematical modeling and statistical analyses of these features. These functionalities permits users to compare treatment and control populations of spheroids. This tool can be used for studying lung cancer spheroids and discriminating different invasive phenotypes.
Determines the red blood cells (RBCs) displacements between pairs of line-scans using spatial cross-correlation analysis. LS-PIV enables quantification of blood velocities from capillaries to high-flow abnormalities deep within the living animal. This method was developed to resolve the spatial profile of simple flows within individual vessels by using multiple line-scans.
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.
Performs spheroid-based high throughput experiments by automatically extracting morphological parameters from bright field images of spheroids. AnaSP allows analysis of spheroids and automatic computation of different morphological parameters, then correlated to the effect of drug dosages and treatments. The tool can be used in high throughput experiments, including high content screening based on spheroids.
A free and open-source tool that complements the object tracking functionality of the CellProfiler biological image analysis package. CellProfiler Tracer allows multi-parametric morphological data to be visualized on object tracks, providing visualizations that have already been validated within the scientific community for time-lapse experiments, and combining them with simple graph-based measures for highlighting possible tracking artifacts.