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Data management and annotation software tools | Bioimaging

Advances in the field of microscopy have brought about the need for better image management and analysis solutions. Novel imaging techniques have created vast stores of images and metadata that are difficult to organize, search, process and…
OMERO.searcher
Desktop
Web

OMERO.searcher

An extension of the OMERO.web client that provides the ability to search for…

An extension of the OMERO.web client that provides the ability to search for images by their content (e.g., subcellular patterns) rather than just by their annotations. It was developed by the Murphy…

OMERO
Desktop
Web

OMERO OME Remote Objects

A software platform that enables access to and use of a wide range of…

A software platform that enables access to and use of a wide range of biological data. OMERO uses a server-based middleware application to provide a unified interface for images, matrices and tables.…

Cytomine
Desktop

Cytomine

An open-source, rich web environment to enable highly collaborative analysis of…

An open-source, rich web environment to enable highly collaborative analysis of multi-gigapixel imaging data. Cytomine (i) provides remote and collaborative principles, (ii) relies on data models…

RPE dataset
Desktop

RPE dataset

A tool which enables image-based classification of maturation of human stem…

A tool which enables image-based classification of maturation of human stem cell-derived retinal pigmented epithelium (RPE). Texture descriptors ensembles are able to classify the RPE cell maturation…

KIRP-topologica…
Desktop

KIRP-topological-features

Automates the characterization of the topological organization of different…

Automates the characterization of the topological organization of different cell patterns in the tumor microenvironment. KIRP-topological-features can learn potential nucleus patterns via an…

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…

CATMAID
Desktop

CATMAID Collaborative Annotation Toolkit for Massive Amounts of Image Data

Allows to navigate, share and collaboratively annotate massive image data sets…

Allows to navigate, share and collaboratively annotate massive image data sets of biological specimens. CATMAID combines three main components: a centralized data server, decentralized image servers…

CamiTK
Desktop

CamiTK Cami ToolKit

Allows researchers and clinicians to collaborate to the elaboration of Computer…

Allows researchers and clinicians to collaborate to the elaboration of Computer Assisted Medical Intervention (CAMI) applications. CamiTK permits to regroup knowledge and expertise in various…

CellMissy
Desktop

CellMissy Cell Migration Invasion Storage System

A cross-platform data management system for cell migration/invasion data that…

A cross-platform data management system for cell migration/invasion data that simplifies and fully automates data management, storage and analysis, from experimental set-up to data visualization and…

Bisque
Desktop
Web

Bisque Bio-Image Semantic Query User Environment

A web-based platform specifically designed to provide researchers with…

A web-based platform specifically designed to provide researchers with organizational and quantitative analysis tools for 5D image data. Users can extend Bisque with both data model and analysis…

Raveler
Desktop

Raveler

Annotates and permits proofreading for large segmented image data. Raveler…

Annotates and permits proofreading for large segmented image data. Raveler capabilities for displaying large image datasets depend of disk storage abilities. The tool was applied to an adult…

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.…

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