Have you ever tried to count sheep when you wanted to fall asleep? It works pretty well in my experience. Did you know that there are many scientists who do this kind of thing for a living? The counting, that is, not the sleeping. Marine biologists, for example. Instead of diving four thousand meters down to the sea floor themselves (good luck with that) they throw robots in the water and let them take ridiculous amounts of images. Then they try to count everything they see in these images—until they fall asleep.

BIIGLE is a web-based software that helps marine biologists (and other people) count as many things as possible in images and videos (… until they fall asleep). This task of looking for things, marking and describing them is referred to as image (and video) annotation. A single annotation consists of two parts, a marker which is a point or a circle, for example, that specifies the position of the object in the image or video, and a label which describes the object.

(ROV Team/GEOMAR, CC-BY 4.0, modified by Martin Zurowietz)Example for an image annotation that consists of a marker and a label.

In BIIGLE, you can upload images and videos and organize them in projects and volumes. These are like directories on your computer. You can also create label trees which are collections of labels that are available for new annotations. Since BIIGLE is a web application, you can invite your colleagues into your annotation projects and annotate together. BIIGLE can handle very large image collections with tens of thousands of images. It can also handle very large images with tens of thousands of pixels on each edge. These are called mosaics because they are stitched together from lots of regular images. While some marine biologists create mosaics for annotation, too, others annotate mosaics created from aerial images or digital microscopy slides. Say goodbye to counting microbes while sitting in the lab hunched over your microscope. With BIIGLE, you can annotate digital slides from the comfort of your favorite armchair and even let your colleagues help you!

(With kind permission by Iguanas from Above) The image annotation tool of BIIGLE that shows annotated iguanas on a large mosaic of aerial images. The minimap at the top right shows the current viewport relative to the whole mosaic.

BIIGLE is developed by the Biodata Mining Group of Bielefeld University, led by Prof. Tim W. Nattkemper. While it was originally created with a focus on marine imaging, it is now used in many other areas as well. Since the source code is open and freely available (at github.com/biigle), several research institutes maintain their own application instances. The Biodata Mining Group maintains the largest public instance at biigle.de which is powered by the de.NBI cloud at Bielefeld University. As of the time this blog post is published, the main instance hosts over 2,000 users from more than 40 countries who created 14 million image and video annotations on 2 million images and videos.

References

• Langenkämper, D., Zurowietz, M., Schoening, T., & Nattkemper, T. W. (2017). BIIGLE 2.0-browsing and annotating large marine image collections. Frontiers in Marine Science, 4, 83.
• Zurowietz, M., Langenkämper, D., & Nattkemper, T. W. (2019, June). BIIGLE2Go—a scalable image annotation system for easy deployment on cruises. In OCEANS 2019-Marseille (pp. 1-6). IEEE.
• Zurowietz, M., & Nattkemper, T. W. (2021). Current trends and future directions of large scale image and video annotation: Observations from four years of BIIGLE 2.0. Frontiers in Marine Science, 1752.