1 - 50 of 70 results

Fiji / Fiji Is Just ImageJ

Focuses on biological image analysis. Fiji serves for the collaboration between computer science and biology research communities. It provides biologists with powerful tools for the generation of advanced image processing pipelines, via scripting languages and feature-rich libraries for processing large quantities of large images, while building upon the simplicity of ImageJ. It is able to deal efficiently with computing intensive tasks on top of large biological image data.


Provides a high-throughput image processing platform. WorMachine enables automated calculation of many morphological and fluorescence features, and accessible machine learning techniques for higher-level features-based analysis, such as classification and phenotype scoring. It combines the capabilities of different programs into one software. The user-friendly interface was designed to suit investigators with no background in MATLAB, image processing, or machine learning, and requires no additional plugins.


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 that allow to easily organize and semantically annotate imaging datasets in a standardized way, (iii) efficiently supports high-resolution multi-gigapixel images, (iv) provides mechanisms to readily proofread and share image quantifications produced by machine learning-based image recognition algorithms.

MITK / Medical Imaging Toolkit

Reduces significantly the effort required to construct specifically tailored, interactive applications for medical image analysis. MITK allows an easy combination of algorithms developed by ITK with visualizations created by VTK and extends these two toolkits with those features, which are outside the scope of both. It adds support for complex interactions with multiple states as well as undo-capabilities, a very important prerequisite for convenient user interfaces.


Provides high quality, well-documented and easy-to-use implementations of common image processing algorithms. Scikit-image is an image processing library that implements algorithms and utilities for use in research, education (by allowing students in image processing to learn algorithms in a hands-on fashion by adjusting parameters and modifying code) and industry applications (High quality reference implementations of trusted algorithms provide industry with a reliable way of attacking problems without having to expend significant energy in re-implementing algorithms already available in commercial packages).

BIDS Apps / Brain Imaging Data Structure Applications

A framework for creating, testing, versioning and archiving portable applications for analyzing neuroimaging data organized and described in compliance with the Brain Imaging Data Structure (BIDS). A BIDS App is a container image capturing a neuroimaging pipeline that takes a BIDS-formatted dataset as input. Each BIDS App has the same core set of command line arguments, making them easy to run and integrate into automated platforms. BIDS Apps are constructed in a way that does not depend on any software outside of the container mage other than the container engine.


Offers a method for discriminating microscopic cancerous imaging. The approach provides a generic computer-aided diagnosis (CAD) framework that consists of two main models: Inception and ResNet. The program permits users to classify cancer types and breast cancer sub-types from histopathological images derived from Hematoxylin and eosin stain (H&E) and Immunohistochemistry (IHC) slides. It also supplies additional techniques for data augmentation and advanced pre-processing.


Supplies a programming interface to the algorithms and data structures of the Insight Segmentation and Registration Toolkit. SimpleITK allows users to implement complex medical image analysis tools and contains a wide range of features for image filtering, segmentation and registration. The application is able to support several transformation types, optimization algorithms, similarity metrics, and interpolators and can be applied to multiple programming languages such as C++, Python, R, Java, C#, Lua, Ruby, and TCL.


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 categories of functions, corresponding to standard image processing workflows: (i) image processing and filtering; (ii) segmentation; (iii) post-processing; (iv) quantitative analysis; (v) library re-usability. The cell-resolved data provided by MorphoLibJ will be useful for the analysis of cell lineage, and the modelling of plant growth and morphogenesis in 3D.

PyBase / Patinopecten yessoensis Database

Gives access to a database of periodic structures of curves on scallop shells. PyBase utilizes image processing analytical methods to classify the data. Bifurcation points, crossover points of the growth rings and ribs and connected lines constitutes the patterns of periodic structures. Species identification is enabled by the individual recognition method. The database permits multiscale segmentation, identification cyclic structures and pattern matching.

MIPAV / Medical Image Processing Analysis and Visualization

Enables quantitative analysis and visualization of medical images of numerous modalities such as PET (positron emission tomography), MRI (magnetic resonance imaging), CT (computerized tomography), or microscopy. Using MIPAV's standard user-interface and analysis tools, researchers at remote sites (via the internet) can easily share research data and analyses, thereby enhancing their ability to research, diagnose, monitor, and treat medical disorders.

VTK / Visualization Toolkit

Allows to generate 3D computer graphics, image processing, and visualization. VTK supports a wide variety of visualization algorithms including scalar, vector, tensor, texture, and volumetric methods, as well as advanced modeling techniques such as implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation. It has an extensive information visualization framework and a suite of 3D interaction widgets. The toolkit supports parallel processing and integrates with various databases on graphical user interface (GUI) toolkits such as Qt and Tk.

MIA / Medical Image Analysis

Provides users libraries and command line tools for the processing and analysis medical images. MIA is a general purpose image processing toolbox that puts its focus on gray scale image processing. This resource provides libraries that can be used to shape newly created algorithms into new command line tools. Various image processing algorithms are also implemented, amongst these specific segmentation algorithms, a variety of image filters and combiners, and generic image registration algorithms.


Processes and analyses electron microscopy (EM) images. Appion is integrated with Leginon data acquisition but can also be used stand-alone after uploading images (either digital or scanned micrographs) or particle stacks using a set of provided tools. Appion consists of a web based user interface linked to a set of python scripts that control several underlying integrated processing packages. All data input and output within Appion is managed using tightly integrated SQL databases. The goal is to have all control of the processing pipeline managed from a web based user interface and all output from the processing presented using web based viewing tools.

Bisque / Bio-Image Semantic Query User Environment

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 extensions in order to adapt the system to local needs. Bisque's extensibility stems from two core concepts: flexible metadata facility and an open web-based architecture. Together these empower researchers to create, develop and share novel bioimage analyses.


Allows image processing of electron micrographs, interpretation of reconstructions, molecular modeling, and general image processing. The Bsoft code is modularized to allow for rapid testing and deployment of new processing algorithms, while also providing sufficient infrastructure to deal with many file formats and parametric data. The design is deliberately open to allow interchange of information with other image and molecular processing software through a standard parameter file and its support of multiple image and molecular formats. The graphical user interface is the program bshow, which is used for many interactive purposes such as fitting the contrast transfer function or picking particles. Bsoft also offers various tools to manipulate atomic structures and to refine the fit of a known molecular structure to a density in a reconstruction.

JIST / Java Image Science Toolkit

Allows users to develop algorithms and to process large-scale images. JIST is a program that generates graphical user interfaces and provides advanced batch processing tools to the scientific community. This software can integrate MIPAV to supply user visualization and exploration of the multi-dimensional imaging data as well as three-dimensional structures. It can be used to encapsulate difficult and time-consuming steps in the analysis and visualization of data from a single subject, or to process data from many subjects.

EMEN / Electron Microscopy Electronic Notebook

Centralizes and mines biological data. EMEN provides an object-oriented database that aims to facilitate the collective management of information into a given structure. The repository provides a system containing individual records with arbitrary additional settings. Users can categorize entries according to four type of access such as read-only or full editing. The application also includes a client: EMDash, that also supplies tools for uploading image processing.


Assists users in analyzing images. ELLIPSE features image manipulation, enhancement, processing, detection and quantitative analysis of multiple objects of interest. It offers several manual and semi-interactive methods built on thresholding or edge-detection of objects. Users can employ several characteristic parameters (such as area, parameter, mean density, roundness etc.) to classify and analyze objects. This software is open to external plug-in modules developed via Plugin Wizard.