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Image segmentation software tools | Bioimaging

Segmentation is one of the fundamental digital image processing operations. It is used ubiquitously across all scientific and industrial fields where imaging has become the qualitative observation and quantitative measurement method.Source…
Vaa3D
Desktop

Vaa3D 3D Visualization-Assisted Analysis

A handy, fast, and versatile 3D/4D/5D image visualization and analysis system…

A handy, fast, and versatile 3D/4D/5D image visualization and analysis system for bioimages and surface objects. Vaa3D also provides many unique functions that you may not find in other software. It…

ImageJ
Desktop

ImageJ

Provides easy installation on arbitrary platforms and a simple user interface.…

Provides easy installation on arbitrary platforms and a simple user interface. ImageJ is a platform for biological image analysis and an open source Java image processing program inspired by NIH…

CellExplorer
Desktop

CellExplorer

A package of computer programs to process and analyze 3D confocal image stacks…

A package of computer programs to process and analyze 3D confocal image stacks of the model animal C. elegans, and can be applied to several other model systems such as fruit fly embryo/larvae as…

Icy
Desktop

Icy

A collaborative bioimage informatics platform that combines a community website…

A collaborative bioimage informatics platform that combines a community website for contributing and sharing tools and material, and software with a high-end visual programming framework for seamless…

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…

fastER
Desktop

fastER fast segmentation with Extremal Regions

Permits cell segmentation based on extremal regions. fastER extracts texture…

Permits cell segmentation based on extremal regions. fastER extracts texture and shape features from candidate regions and estimates the likelihood of each to be a cell with a support vector machine…

CellStar
Desktop

CellStar

Permits analysis of video microscopy data for long-term experiments. CellStar…

Permits analysis of video microscopy data for long-term experiments. CellStar has been designed to achieve good performance and was compared with six software solutions dedicated to yeast cell…

GALA
Desktop

GALA Graph-based Active Learning of Agglomeration

Provides state of the art automatic segmentation accuracy for image…

Provides state of the art automatic segmentation accuracy for image segmentation. GALA utilises machine learning to obtain a merge priority function or policy, which dictates which pair of segments…

LEVER
Desktop

LEVER

A software tool for lineage editing and validation. LEVER segments, tracks and…

A software tool for lineage editing and validation. LEVER segments, tracks and lineages time lapse microscopy image sequences of live stem cells. LEVER works in 2-D and 3-D and with phase and…

3D Slicer
Desktop

3D Slicer

Allows medical image computing and visualization. 3D Slicer is an open source…

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…

Patternize
Desktop

Patternize

Allows image alignment and segmentation and can quantify color patterns in a…

Allows image alignment and segmentation and can quantify color patterns in a wide range of organisms. Patternize can be used for quantification of the color patterns in a variety of organisms by…

TWS
Desktop

TWS Trainable Weka Segmentation

Permits to classify pixels. TWS can be used for a wide range of applications…

Permits to classify pixels. TWS can be used for a wide range of applications such as boundary detection, semantic segmentation, or object detection and localization. It transforms the segmentation…

SuRVoS
Desktop

SuRVoS Super-Region Volume Segmentation

Combines the human expert’s knowledge with data representation, machine…

Combines the human expert’s knowledge with data representation, machine learning and active learning techniques. SuRVos works according to these steps: (1) Data Preparation, (2) Data Preprocessing,…

CP-CHARM
Desktop

CP-CHARM

A user-friendly image-based classification algorithm inspired by WND-CHARM in…

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…

HMSLIC
Algorithm
Soma-Segmentati…
Desktop

Soma-Segmentation

Allows analysis of morphology quantification. Soma-Segmentation contains three…

Allows analysis of morphology quantification. Soma-Segmentation contains three main parts: (1) soma detection based on distance transform (DT) and local maximum searching and refining; (2) an…

MorphoLibJ
Desktop

MorphoLibJ

Proposes a large collection of generic tools based on mathematical morphology…

Proposes a large collection of generic tools based on mathematical morphology to process binary and grey-level 2D and 3D images, integrated into user-friendly plugins. The library provides different…

RAZA
Desktop

RAZA RApid 3D Z-crossings Algorithm

Segments low signal-to-noise ratio (SNR) data typical of 3D reconstructed…

Segments low signal-to-noise ratio (SNR) data typical of 3D reconstructed volumes. RAZA is a detection algorithm that integrates a Laplacian of Gaussian (LoG) kernel, with arbitrary z-crossings and…

MaEtAl2017
Algorithm

MaEtAl2017

Allows users to segment the prostate on computerized tomography (CT) images.…

Allows users to segment the prostate on computerized tomography (CT) images. This approach combines the population learning and patient-specific learning together for segmenting the prostate on 3D CT…

FluoRender
Desktop

FluoRender

Allows to visualize confocal microscopy data. FluoRender can preserve original…

Allows to visualize confocal microscopy data. FluoRender can preserve original fluorescence intensity values on graphics hardware and supports far more than three Red-Green-Blue (RGB) channels. It…

Spectral…
Desktop

Spectral Imaging Toolbox

Measures accurately cell membrane lipid packing without cytosolic contributions…

Measures accurately cell membrane lipid packing without cytosolic contributions using a single dye. The Spectral Imaging Toolbox was designed for spectral analysis of high magnification images of…

MLTM
Desktop

MLTM

Contains a semisupervised multi-instance (MI) learning method for multilabel…

Contains a semisupervised multi-instance (MI) learning method for multilabel classification. MLTM is a multilabel topic model that discovers a set of M topics (latent structure in the data) and…

CellAging
Desktop

CellAging

Extracts information on polar segregation and partitioning in division of…

Extracts information on polar segregation and partitioning in division of aggregates in E. coli and on cellular vitality. CellAging creates seeds from cells segmented and then applies the…

FMAj
Desktop

FMAj Fly Muscle Analysis in Java

Performs quantitative characterization of muscle phenotypes in time-series…

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…

SIMA
Desktop

SIMA Sequential IMage Analysis

Facilitates common analysis tasks related to fluorescence imaging.…

Facilitates common analysis tasks related to fluorescence imaging. Functionality SIMA includes correction of motion artifacts occurring during in vivo imaging with laser-scanning microscopy,…

Voxx
Desktop

Voxx

Allows to explore complex microscopy data. Voxx is a volume visualization…

Allows to explore complex microscopy data. Voxx is a volume visualization software provides interactive inspection and manipulation of 3D images on personal computers (PCs). The software renders set…

VNet
Desktop

VNet

Allows users to perform biomedical volumetric segmentation thanks to a…

Allows users to perform biomedical volumetric segmentation thanks to a volumetric convolutional neural network approach. VNet is a program, based on a customized version of the caffe software, which…

U-Net
Desktop

U-Net

Allows users to perform biomedical segmentation, including volumetric tasks.…

Allows users to perform biomedical segmentation, including volumetric tasks. U-Net is open source program, based on a modification of the caffe software, that segments 2D and 3D data. It implements…

SimVascular
Desktop

SimVascular

Allows users to perform image-based hemodynamics simulation. SimVascular is an…

Allows users to perform image-based hemodynamics simulation. SimVascular is an open source software which provides a pipeline from model construction to simulation analysis. The software authorizes…

FigSplit
Web

FigSplit

Segments compound images appearing in biomedical documents. FigSplit is a…

Segments compound images appearing in biomedical documents. FigSplit is a Connected Component Analysis (CCA)-based scheme for segmenting compound images, including stitched compound images, while…

Anglegram
Algorithm

Anglegram

Allows to realize automatic segmentation of overlapping cells. Anglegram…

Allows to realize automatic segmentation of overlapping cells. Anglegram identifies junctions between the boundaries of overlapping objects based on the angles between points of the overlapping…

DeepEM3D
Desktop

DeepEM3D

Represents a deep learning method for segmenting 3D anisotropic brain electron…

Represents a deep learning method for segmenting 3D anisotropic brain electron microscopy images. DeepEM3D can efficiently build feature representation and incorporate sufficient multi-scale…

Cell-Imaging
Desktop

Cell-Imaging

Evaluates and compares the performance levels of Cell image segmentation (CIS)…

Evaluates and compares the performance levels of Cell image segmentation (CIS) algorithms with statistical confidence. Cell-Imaging uses significance values for differences in CIS algorithm…

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…

NeuroProof
Desktop

NeuroProof

Permits to reconstruct complete connectome. NeuroProof is based on a threshold…

Permits to reconstruct complete connectome. NeuroProof is based on a threshold k determined heuristically. It is amenable to large-scale, crowd-sourcing efforts. The tool was used in the domain of…

GemIdent
Desktop

GemIdent

Recognizes cell in microscopic images. GemIdent supports standard RGB images,…

Recognizes cell in microscopic images. GemIdent supports standard RGB images, for image sets derived from the Bacus Laboratories Incorporated Slide Scanner and the CRI Nuance Multispectral Imager. It…

IFDOTMETER
Desktop

IFDOTMETER

Quantifies biological hallmarks and includes mitochondrial morphology and…

Quantifies biological hallmarks and includes mitochondrial morphology and nuclear condensation. IDOTMETER allows to measure a variety of cellular changes, mainly involving autophagy and cell survival…

Signature
Desktop

Signature

Provides a particle data analysis system for macromolecule electron microscopy…

Provides a particle data analysis system for macromolecule electron microscopy (EM). Signature hosts a particle screening module and a particle analysis module. The graphic user interface of the…

BrainSeg3D
Desktop

BrainSeg3D

Provides a free volume (3D image) viewer and segmentation tool. BrainSeg3D is a…

Provides a free volume (3D image) viewer and segmentation tool. BrainSeg3D is a graphic application that make segmentation of volumes more accurate by providing tools for semi-automated segmentation…

iCut
Algorithm

iCut integrative Cut

Segments touching cells in 2D images. iCut provides an integrative cut…

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…

Spot Detector
Desktop

Spot Detector

Allows to detect spots in different conditions. Spot Detector can find spots in…

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…

CRImage
Desktop

CRImage

Provides image analysis tools for segmentation, classification, and downstream…

Provides image analysis tools for segmentation, classification, and downstream analysis of tumour section images. CRImage is a Bioconductor package that allows cellularity scoring of tumours which…

VAST
Desktop

VAST Volume Annotation and Segmentation Tool

Allows manual annotation and segmentation of large volumetric (voxel) data…

Allows manual annotation and segmentation of large volumetric (voxel) data sets. VAST is a software which enables to work with voxel data sets in the Terabyte or even Petabyte range at interactive…

GridMos
Desktop

GridMos

Allows to obtain a mosaic representing the whole hemocytometer’s grid.…

Allows to obtain a mosaic representing the whole hemocytometer’s grid. GridMos is a computer vision-based approach to improve reproducibility (inter-rater reliability) and repeatability…

Simpleware…
Desktop

Simpleware ScanIP

Provides a software environment for comprehensively processing 3D image data…

Provides a software environment for comprehensively processing 3D image data (MRI, CT, micro-CT, FIB-SEM…). Simpleware ScanIP offers powerful image visualisation, analysis, segmentation, and…

Bioimagetools
Desktop

Bioimagetools

Provides tools for bioimaging like 3D binary segmentation, function to compute…

Provides tools for bioimaging like 3D binary segmentation, function to compute the distance from spots to borders of classes or filter applied to a 3D array representing an image. An amount of 19…

CellSegm
Desktop

CellSegm

A MATLAB based command line software toolbox providing an automated whole cell…

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…

FogBank
Desktop

FogBank

An automated segmentation method that accurately separates cells when confluent…

An automated segmentation method that accurately separates cells when confluent and touching each other. This technique is successfully applied to phase contrast, bright field, fluorescence…

BoneJ
Desktop

BoneJ

A plugin for bone image analysis in ImageJ. BoneJ provides free, open source…

A plugin for bone image analysis in ImageJ. BoneJ provides free, open source tools for trabecular geometry and whole bone shape analysis. It calculates several trabecular, cross-sectional and…

SMASH
Desktop

SMASH Semi-automatic Muscle Analysis using Segmentation of Histology

Provides an automatic and standardized image segmentation platform. SMASH…

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…

LSDCAS
Desktop

LSDCAS Large Scale Digital Cell Analysis System

An extensible, automated system for high throughput screening and…

An extensible, automated system for high throughput screening and non-perturbing optical single cell analysis. The analytical capabilities of LSDCAS include automatic cell motility analysis, and the…

CellSegmentatio…
Desktop

CellSegmentation3D

An automated algorithm for 3D cell nuclei segmentation based on gradient flow…

An automated algorithm for 3D cell nuclei segmentation based on gradient flow tracking. The proposed algorithm is able to segment closely juxtaposed or touching cell nuclei obtained from 3D…

CoreHist
Web

CoreHist

Provides a cloud-based web-server designed to implement correlation filter…

Provides a cloud-based web-server designed to implement correlation filter based detector. CoreHist is based on a method that use kernelized correlation filter for nuclei detection in histopathology…

pyBioImage
Desktop

pyBioImage

Allows users to estimate Germinal Center (GC) volumes from standard…

Allows users to estimate Germinal Center (GC) volumes from standard multidimensional image data. pyBioImage is a cross-platform bioimaging application which supports several data formats and provides…

STAPLE
Algorithm

STAPLE Simultaneous Truth And Performance Level Estimation

Provides estimates of performance parameters accounting for external standard…

Provides estimates of performance parameters accounting for external standard reference. STAPLE is an algorithm for taking a collection of both binary and unordered multicategory segmentations. It…

HabitApp
Desktop
Mobile

HabitApp

Computes percentage cover using a photo of the canopy. HabitApp is a tool able…

Computes percentage cover using a photo of the canopy. HabitApp is a tool able to convert pixels to black and white. It includes cut-off value which determines if pixel becomes black or white,…

LiuEtAl2007
Desktop

LiuEtAl2007

Assists in quantification of zebrafish neuronal cells. This tool consists in…

Assists in quantification of zebrafish neuronal cells. This tool consists in four stages: (1) it produces a diffused gradient vector field; (2) it calculates a response image; (3) it performs…

Imaris
Desktop

Imaris

Allows users to manage image data, results and derived data, and image analysis…

Allows users to manage image data, results and derived data, and image analysis protocols. Imaris permits to tag resources as a search across all experiments or a specific set of experimental groups.…

Webimg
Desktop

Webimg

Allows to analyze images and permits image segmentation or edge detection.…

Allows to analyze images and permits image segmentation or edge detection. Webimg offers a way to analyse an image by using the fastest method.

NiftySeg
Desktop

NiftySeg

Performs electron microscopy (EM) based segmentation of images in nifti or…

Performs electron microscopy (EM) based segmentation of images in nifti or analyse format. NiftySeg contains a package of label fusion algorithms (MV, STAPLE, SBA) with different types of ranking…

Amira 3D…
Desktop

Amira 3D Software for Life Sciences

Allows users to visualize, manipulate, and understand data from imaging…

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…

CyteSeer
Desktop

CyteSeer

Analyzes images from almost any digital fluorescent microscope or high-content…

Analyzes images from almost any digital fluorescent microscope or high-content screening device. CyteSeer is an automated cell image analysis software that provides powerful data analysis, gating and…

Free-D
Desktop

Free-D

A three-dimensional (3D) reconstruction and modeling software. Free-D allows to…

A three-dimensional (3D) reconstruction and modeling software. Free-D allows to generate, process and analyze 3D point and surface models from stacks of 2D images. It is an integrated software tool,…

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…

CellTracer
Desktop

CellTracer

An integrated graphical user interface written in MATLAB that implements…

An integrated graphical user interface written in MATLAB that implements methods for automating cell segmentation/lineage reconstruction. The automated analysis iteratively combines a set of extended…

Acapella High…
Desktop

Acapella High Content Imaging and Analysis Software

Provides rapid online image data processing and thoroughly flexible analysis…

Provides rapid online image data processing and thoroughly flexible analysis for all high content cellular applications, including multi-parametric multiplex assays. It’s the driving force behind…

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