Anchor is a free command-line application and platform for image analysis, especially microscopy image analysis.

It’s a Swiss-army-knife for loading, transforming, and extracting information from sets of images, as single-image tools are often limiting.


Anchor logo

  • Supports diverse image types and formats (photos, 2D / 3D / time-series microscopy).
  • Smartly names outputs by finding patterns in filenames. Preserves directory structure.
  • Reproducible pipelines defined via XML.
  • Feature-extraction libraries (sets of voxels, geometric shapes) etc.
  • Extensible via Java to call operations in ImageJ, Icy, OpenCV etc.
  • Cross-platform - Windows, Linux, Mac - with seemless switching between local and server.
  • A basic pinboard-style GUI for images, segmentations and features.

Project Status

Anchor’s source-code can be found on GitHub. It is a significant project, covering 170,000 lines-of-code across 3,600 Java classes, as well as BeanXML analysis pipelines.

Effort is ongoing to create documentation and address technical debt for the first formal public release. Only a pre-alpha distribution can be downloaded until then.


Owen Feehan - developed since 2010 across employment in ETH Zurich, the University of Zurich and Hoffmann-La Roche. Licensed open source.