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Image cytometry software tools | Bioimaging

SFSRR
Desktop

SFSRR

Recovers accurate quantitative radioactivity concentration in Positron Emission…

Recovers accurate quantitative radioactivity concentration in Positron Emission Tomography (PET) images. SFSRR combines functional and structural information from a number of sources such as…

BROCCOLI
Desktop

BROCCOLI

Can process parallel analysis of functional magnetic resonance imaging (fMRI)…

Can process parallel analysis of functional magnetic resonance imaging (fMRI) data on a large variety of hardware configurations. BROCCOLI can perform non-linear spatial normalization to a 1 mm3…

MANTiS
Desktop

MANTiS Morphologically Adaptive Neonatal Tissue Segmentation

Extends the unified segmentation approach to tissue classification implemented…

Extends the unified segmentation approach to tissue classification implemented in Statistical Parametric Mapping (SPM) software to neonates. MANTiS utilizes a combination of unified segmentation,…

Heteroscedastic…
Desktop

HeteroscedasticfMRI

Permits to analyze functional magnetic resonance imaging (fMRI) data.…

Permits to analyze functional magnetic resonance imaging (fMRI) data. HeteroscedasticfMRI is based on a Markov Chain Monte Carlo (MCMC) algorithm. It allows for Bayesian variable selection among the…

flowFit
Desktop

flowFit

Performs quantitative analysis of cell proliferation in tracking dye-based…

Performs quantitative analysis of cell proliferation in tracking dye-based experiments. flowFit, distributed as an R Bioconductor library, is based on a mathematical model that takes into account the…

histoCAT
Web

histoCAT HIStology TOpography Cytometry Analysis Toolbox

Uses a computational multiplexed image cytometry analysis toolbox to enable the…

Uses a computational multiplexed image cytometry analysis toolbox to enable the interactive, quantitative, and comprehensive exploration of phenotypes of individual cells, cell-to-cell interactions,…

FreeSurfer
Desktop

FreeSurfer

Allows the analysis and visualization of structural and functional neuroimaging…

Allows the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. FreeSurfer proposes a suite of tools that provide extensive and…

Schnitzcells
Desktop

Schnitzcells

A MATLAB based software that allows for quantitative analysis of fluorescent…

A MATLAB based software that allows for quantitative analysis of fluorescent time-lapse movies of living cells.

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.

ACTIVE
Desktop
GenoSIGHT
Desktop

GenoSIGHT

An imaging system package relying on a closed-loop control algorithm to adapt…

An imaging system package relying on a closed-loop control algorithm to adapt the collection of a series of time-lapse images to optimize the measurement of gene expression data in individual cells.…

BrainVISA
Desktop

BrainVISA

Hosts heterogeneous tools dedicated to neuroimaging research. BrainVISA aims to…

Hosts heterogeneous tools dedicated to neuroimaging research. BrainVISA aims to help researchers in developing new neuroimaging tools, sharing data and distributing software. It offers a way to…

TLM-Tracker
Desktop

TLM-Tracker Time-Lapse-Movie-Tracker

A free platform independent tool for single cell analyses in live-cell imaging…

A free platform independent tool for single cell analyses in live-cell imaging experiments like time lapse microscopy.

CLOCCS
Desktop

CLOCCS Characterizing Loss of Cell Cycle Synchrony

A flexible mathematical model that describes the dynamics of population…

A flexible mathematical model that describes the dynamics of population distributions resulting from synchrony loss over time.

TACTICS
Desktop

TACTICS

A modular MATLAB(R) Toolbox for time-lapse image analysis.

A modular MATLAB(R) Toolbox for time-lapse image analysis.

ACME
Desktop

ACME Automated Cell Morphology Extraction

Open-source C++ software for reconstructing membranes to achieve high-quality…

Open-source C++ software for reconstructing membranes to achieve high-quality whole cell segmentations.

iTrack4U
Desktop

iTrack4U

A Java-based software using ImageJ and jMathPlot libraries, which aims at…

A Java-based software using ImageJ and jMathPlot libraries, which aims at automatically tracking cells recorded in phase-contrast microscopy.

IMIRS
Desktop

IMIRS Image Management and Icosahedral Reconstruction System

Consists of a complete set of modular programs for icosahedral reconstruction…

Consists of a complete set of modular programs for icosahedral reconstruction organized under a graphical user interface. IMIRS provides options for user-friendly, step-by-step data processing 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.

libics
Desktop

libics

Allows users to build Image Cytometry Standard (ICS) applications. libics is…

Allows users to build Image Cytometry Standard (ICS) applications. libics is the reference library for ICS, a standard for writing images in any dimensiona and data type file, together with…

CellOrganizer
Desktop

CellOrganizer

Provides tools for learning generative models of cell organization directly…

Provides tools for learning generative models of cell organization directly from images, storing and retrieving those models in XML files and synthesizing cell images (or other representations) from…

ACE
Desktop

ACE Automated CTF Estimation

Provides a completely automated method for the estimation of the contrast…

Provides a completely automated method for the estimation of the contrast transfer function (CTF), the envelope function and the noise spectrum parameters of an image taken using transmission…

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