A collection is a software that encapsulate a set of bioimage components and/or workflows.

elastix

Bioimage Analyst
Developer

Elastix is a toolbox for rigid and nonrigid registration of (medical) images.

Elastix is based on the ITK library, and provides additional algorithms for image registration. 

The software can be run as a single-line command, making it easy to include in larger scripts or workflows. The user needs to edit a configuration file that contains all relevant parameters for registration: transformation model, metric used to comapre images, optimization algorithm, mutliscale pyramidal representation of images...

Orbit

Bioimage Analyst
Developer

Orbit Image Analysis is a free open source software with the focus to quantify big images like whole slide scans.

It can connect to image servers, e.g. Omero.
Analysis can be done on your local computer or via scaleout functionality in a distrubuted computing environment like a Spark cluster.

Sophisticated image analysis algorithms incl. tissue quantification using machine learning, object segmentation and classification are build in. In addition a versatile API allows you to enhance Orbit and to run your own scripts.

CEM

Biologist
Microscopist

Computer-assisted Evaluation of Myelin formation (CEM) is a collection designed to automate myelin quantification. It requires use input to choose the best threshold values. The myelin is calculated as an overlap between neuronal signal and oligodendrocyte signal. Results are given as pixel counts and percents.

MIPAV

Bioimage Analyst
Developer

The MIPAV (Medical Image Processing, Analysis, and Visualization) application enables quantitative analysis and visualization of medical images of numerous modalities such as PET, MRI, CT, 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.