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Cell tracking software tools | Laser scanning microscopy

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…
CellCognition
Desktop

CellCognition

A computational framework to annotate complex cellular dynamics. A…

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…

NeRVEclustering
Desktop

NeRVEclustering Neuron Registration Vector Encoding

Allows to track populations of neurons with single neuron resolution in the…

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…

tTt
Desktop

tTt The Tracking Tool

Allows quantification of cellular and molecular properties and single-cell…

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…

CellX
Desktop

CellX

A tool for segmentation, fluorescence quantification, and tracking of cells on…

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…

EBImage
Desktop

EBImage

Provides general purpose functionality for reading, writing, processing and…

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…

ParticleStats
Desktop
Web

ParticleStats

A web server and open source programs, which input the X, Y coordinate…

A web server and open source programs, which input the X, Y coordinate positions of objects in time, and output novel analyses, graphical plots and statistics for motile objects.

FijiWingsPolari…
Desktop

FijiWingsPolarity

Measures automatically trichome orientation in the Drosophila wing using…

Measures automatically trichome orientation in the Drosophila wing using several integrated functions. FijiWingsPolarity is a set of macro tools designed to analyze the orientation of trichomes in…

PolNet
Desktop

PolNet

Serves for network-level quantitative research in vascular morphogenesis.…

Serves for network-level quantitative research in vascular morphogenesis. PolNet can quantify the relationship between endothelial cell polarity and wall shear stress (WSS). The software uses…

EpiTools
Desktop

EpiTools

Allows analysis of epithelial tissues. EpiTools automates image analysis…

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…

TissueMiner
Desktop

TissueMiner

Allows users to understand the creation of tissue dynamics by cellular…

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…

CellProfiler…
Desktop

CellProfiler Tracer

A free and open-source tool that complements the object tracking functionality…

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…

ACTIVE
Desktop

ACTIVE Automated Contour-based Tracking for In Vitro Environments

Useful to researchers who require accurate, long-time-scale motility data for…

Useful to researchers who require accurate, long-time-scale motility data for many cells.

Aivia
Desktop

Aivia

Combines state-of-the-art automated neuron tracing and machine learning-enabled…

Combines state-of-the-art automated neuron tracing and machine learning-enabled neuron classification tools. Aivia provides methods for analyzing time-lapse images. It covers a wide range of…

CellTrack
Desktop

CellTrack

A self-contained, extensible, and cross-platform software package for cell…

A self-contained, extensible, and cross-platform software package for cell tracking and motility analysis.

AnaSP
Desktop

AnaSP

Performs spheroid-based high throughput experiments by automatically extracting…

Performs spheroid-based high throughput experiments by automatically extracting morphological parameters from bright field images of spheroids. AnaSP allows analysis of spheroids and automatic…

TRAgen
Desktop

TRAgen Track generator

Generates 2D image sequences that show simulated living cell populations.…

Generates 2D image sequences that show simulated living cell populations. TRAgen creates GT-enabled image sequences with vast amounts of cells highlithing several tracking events, such as cells…

TIKAL
Desktop

TIKAL

A 4-D image processing platform for the work with laser scanning and wide field…

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…

Cell_motility
Desktop

Cell_motility

An open source Java application under the GNU-GPL license that provides a clear…

An open source Java application under the GNU-GPL license that provides a clear and concise analysis workbench for large amounts of cell motion data.

Huygens
Desktop

Huygens

Restores images from microscopic data. Huygens is based on the deconvolution…

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…

DiaTrack
Desktop

DiaTrack

Benchmark object tracking software for 2D and 3D applications, such as…

Benchmark object tracking software for 2D and 3D applications, such as biological imaging, rheology, or single molecule imaging. DiaTrack provides a compelling set of tools to extract quantitative…

Quimp
Desktop

Quimp

A method to correlate local cortical fluorescence with membrane movement. It…

A method to correlate local cortical fluorescence with membrane movement. It has a completely new semi-automated segmentation interface, a greatly improved boundary tracking method based on Richard…

SpotTracker
Desktop

SpotTracker

A robust and fast computational procedure for tracking fluorescent markers in…

A robust and fast computational procedure for tracking fluorescent markers in time-lapse microscopy. The algorithm is optimized for finding the time-trajectory of single particles in very noisy image…

TLA
Desktop

TLA Time Lapse Analyser

A free, cross-platform, open source software for high throughput time-lapse…

A free, cross-platform, open source software for high throughput time-lapse data processing for live cell imaging. TLA is a graphical tool which enables easy access to high-throughput live cell…

DcellIQ
Desktop

DcellIQ Dynamic Cell Image Quantitator

Aims to provide an automated pipeline for quantitative, reproducible and…

Aims to provide an automated pipeline for quantitative, reproducible and accurate interpretation of cell dynamic behaviors using time-lapse cellular images. DCellIQ is an automated tool with several…

LineageTracker
Desktop

LineageTracker

Offers an ImageJ based framework which is easily extendible and has the…

Offers an ImageJ based framework which is easily extendible and has the capability to track cell lineages while being specifically designed to handle large cell displacements between frames. The…

Mtrack2
Desktop

Mtrack2

It is based on the MultiTracker plugin by Jeffrey Kuhn which is based on the…

It is based on the MultiTracker plugin by Jeffrey Kuhn which is based on the Object tracker plugin by Wayne Rasband. In contrast to the Multitracker plugin, the number of objects may vary between…

Volocity
Desktop

Volocity

Provides all the tools you need to visualize, analyze and validate 3D…

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…

MetaMorph
Desktop

MetaMorph

It is the ideal "glue" for easily integrating dissimilar fluorescent…

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…

ilastik
Desktop

ilastik

A simple, user-friendly tool for interactive image classification, segmentation…

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)…

FARSIGHT
Desktop

FARSIGHT

It is an organized collection of software modules for image data handling,…

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…

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