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High-throughput screening | Bioimaging software tools

Millions of cells are present in thousands of images created in high-throughput screening (HTS). Biologists could classify each of these cells into a phenotype by visual inspection. But in the presence of millions of cells this visual classification…
PhenoRipper
Desktop

PhenoRipper

Allows user to explore high-content microscopy images. PhenoRipper assists…

Allows user to explore high-content microscopy images. PhenoRipper assists users in comparison of images and based on similarity of image phenotypes. It uses cluster analysis to identify superblock…

ViBE-Z
Web

ViBE-Z Virtual Brain Explorer for Zebrafish

An imaging and image analysis framework for virtual colocalization studies in…

An imaging and image analysis framework for virtual colocalization studies in larval zebrafish brains. ViBE-Z contains a database with precisely aligned gene expression patterns, an anatomical atlas,…

BioImageXD
Desktop

BioImageXD

Analyzes, processes and visualizes multi-dimensional microscopy images.…

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…

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…

PhenoPlot
Desktop

PhenoPlot

Allows representation of multidimensional cellular measurements. PhenoPlot is a…

Allows representation of multidimensional cellular measurements. PhenoPlot is a toolbox that permits visualization of up to 21 variables. It may be useful for determining the morphology of breast…

IEV
Web

IEV Interactive Embryo Viewer

Allows users to directly compare wild-type and mutant embryos in a dynamic,…

Allows users to directly compare wild-type and mutant embryos in a dynamic, intuitive manner. With IEV, users can navigate the volumes in synchrony by using the sliders, mouse wheel or crosshair tool…

Mineotaur
Web

Mineotaur

Allows easy online sharing and interactive visualisation of large screen…

Allows easy online sharing and interactive visualisation of large screen datasets, facilitating their dissemination and further analysis, and enhancing their impact. The user interface allows the…

IMPC
Dataset

IMPC International Mouse Phenotyping Consortium

Provides the biomedical community with a unified point of access to mutant mice…

Provides the biomedical community with a unified point of access to mutant mice and rich collection of related emerging and existing mouse phenotype data. IMPC mouse clinics worldwide follow rigorous…

CPA
Desktop

CPA CellProfiler Analyst

A software for biological image-based classification, data exploration, and…

A software for biological image-based classification, data exploration, and visualization designed for biologists and data scientists. CellProfiler Analyst builds on these features and adds enhanced…

Cellgraphs
Desktop

Cellgraphs

An automatic analysis of complete whole slide images (WSIs) to determine…

An automatic analysis of complete whole slide images (WSIs) to determine significant morphological and immunohistochemical features of Hodgkin lymphoma (HL) cells and their spatial distribution in…

ACC
Desktop

ACC Advanced Cell Classifier

Offers access to a variety of advanced machine learning methods and provides an…

Offers access to a variety of advanced machine learning methods and provides an accurate high-content screen analysis. Advanced Cell Classifier (ACC) contains two features: (1) it is not limited to a…

VPV
Desktop

VPV Volume Phenotype Viewer

Enables rapid identification of phenotypically abnormal structures. Data are…

Enables rapid identification of phenotypically abnormal structures. Data are easily loaded by drag and drop, with support for most commonly used file formats. On loading the registration results,…

HARP
Desktop

HARP Harwell Automated Reconstruction Processor

An open-source, cross-platform application. HARP is designed to operate on 3D…

An open-source, cross-platform application. HARP is designed to operate on 3D image data represented as two-dimensional (2D) slices in a variety of formats (tiff, bmp, jpg, etc.). Although it was…

HTX
Desktop

HTX High-Throughput eXplorer

Aids in the exploration of large microscopy data. HTX is a computer vision and…

Aids in the exploration of large microscopy data. HTX is a computer vision and machine learning pipeline that allows users to visualize the entire image-based assays according to visual similarities…

CellCognition…
Desktop

CellCognition Explorer

Represents a generic novelty detection and deep learning framework which can…

Represents a generic novelty detection and deep learning framework which can enables sensitive and accurate cellular phenotype detection. CellCognition Explorer serves for integrated data analysis…

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…

Blood Analysis…
Mobile

Blood Analysis App

Detects and concentrates estimation of various bio-markers in blood sample…

Detects and concentrates estimation of various bio-markers in blood sample images. Blood Analysis App is an Android application which allows the user to take images of the blood samples in a set…

VisBio
Desktop

VisBio

Designed for easy visualization and analysis of multidimensional image data.…

Designed for easy visualization and analysis of multidimensional image data. VisBio software is an end-user application built from the ground up to handle visualization and analysis of…

L1H
Desktop

L1H L1-Homotopy

Analyzes high-density 2D STORM data using compressed sensing. For an…

Analyzes high-density 2D STORM data using compressed sensing. For an experimental data set with varying emitter density, L1H analysis is ~300-fold faster than interior point methods. This drastic…

BIOCAT
Desktop

BIOCAT BIOimage Classification and Annotation Tool

It is able to apply pattern recognition algorithms to two- and…

It is able to apply pattern recognition algorithms to two- and three-dimensional biological image sets as well as regions of interest (ROIs) in individual images for automatic classification and…

cellXpress
Desktop

cellXpress

A fast and user-friendly software platform to segment cells, measure…

A fast and user-friendly software platform to segment cells, measure quantitative features of cellular phenotypes, construct discriminative profiles, and visualize the resulting cell masks and…

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…

WND-CHARM
Desktop

WND-CHARM

A multi-purpose image classifier that can be applied to a wide variety of image…

A multi-purpose image classifier that can be applied to a wide variety of image classification tasks without modifications or fine-tuning, and yet provides classification accuracy comparable to…

ECC
Desktop

ECC Enhanced CellClassifier

Allows multiple class classification, elucidating complex phenotypes. Enhanced…

Allows multiple class classification, elucidating complex phenotypes. Enhanced CellClassifier is designed for the biologist who wants both, simple and flexible analysis of images without requiring…

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