This is the application manual of BIIGLE. Here you can find articles on how to use the application as well as reference publications and the developer documentation.
Learn how you can manage your user account.
View and manage BIIGLE notifications in the notification center.
Learn what projects are and how to manage them.
Learn what label trees are and how you can manage them.
Learn how to create, modify or delete labels of a label tree.
Everything you need to know about versioned label trees.
View and resolve differences between label trees.
The annotation catalog shows you all annotations with a certain label.
Learn more on how you can download a label tree and use it elsewhere.
The volume overview allows you to explore all images that belong to a volume.
With remote volumes you can use images from your own data source in BIIGLE.
Annotation sessions can be used to conduct scientific studies.
Upload image metadata to add information that can't be extracted from the images.
Image labels are labels that are attached to whole images.
A quick introduction to the annotation tool.
Learn about all the tools that are available to create new annotations.
Learn about all the tools to modify or delete existing annotations.
Learn about advanced ways to navigate the images in the annotation tool.
All sidebar tabs of the annotation tool explained.
A list of all available shortcut keys in the annotation tool.
Advanced configuration of the annotation tool.
The Label Review Grid Overview and what you can do with it.
A description of the file formats of the different available reports.
The volume map shows the locations of images on a world map.
The automatic laser point detection is used to determine the visual footprint of images.
Learn how to ask any person for advice on the label of an annotation.
An introduction to the Machine Learning Assisted Image Annotation method (MAIA).
A description of the first MAIA stage and the configurable parameters.
A description of the second MAIA stage.
A description of the third MAIA stage and the configurable parameters.
A description of the last MAIA stage.
An introduction to the video annotation tool.
Learn how to create different kinds of video annotations.
Learn about the video timeline and how to navigate it.
Learn about all the tools to modify or delete existing video annotations.
All sidebar tabs of the video annotation tool explained.
A list of all available shortcut keys in the video annotation tool.
Advanced configuration of the video annotation tool.
With remote videos you can use videos from your own data source in BIIGLE.
Reference publications that you should cite if you use BIIGLE for one of your studies.
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. doi:
Laser Point Detection
Schoening, T., Kuhn, T., Bergmann, M., & Nattkemper, T. W. (2015). DELPHI—fast and adaptive computational laser point detection and visual footprint quantification for arbitrary underwater image collections.
Frontiers in Marine Science, 2, 20. doi:
Zurowietz, M., Langenkämper, D., Hosking, B., Ruhl, H. A., & Nattkemper, T. W. (2018). MAIA—A machine learning assisted image annotation method for environmental monitoring and exploration.
PloS one, 13(11), e0207498. doi:
Video Object Tracking
Lukezic, A., Vojir, T., ˇCehovin Zajc, L., Matas, J., & Kristan, M. (2017). Discriminative correlation filter with channel and spatial reliability. In Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition (pp. 6309-6318). doi:
The source code of BIIGLE can be found at GitHub.
You may access most of the functionality of this application using the RESTful API. Most of the API requires user authentication via session cookie (being logged in to the website) but it is also available for external requests using a personal API token. You can manage your API tokens in the user settings.
The API works with form (
x-www-form-urlencoded) as well as JSON requests. For form requests, you can use method spoofing to use different HTTP methods. For the complete documentation, check out the link below.
The server application is written in PHP using the Laravel framework. Have a look at their excellent documentation for further information. For the class reference and API documentation, check out the link below.
Laravel allows a modular application design using custom packages (or modules). In fact, the core of this application doesn't provide much more than user and database management as well as the RESTful API. Any additional functionality is added by a new module.
We encourage you to add functionality by developing your own modules! There are some resources on package development in the Laravel documentation but we have some tutorials here as well.
The database schema documentation can be found in the BIIGLE GitHub organization.
Learn about PHP package development and how to add custom functionality to your BIIGLE installation by developing your own modules.
Learn how to add new views and routes with a custom package and how to properly test them using the BIIGLE testing environment.
Building your custom extensions is nice but what about extending the extensions? Learn how to use the view mixin registry of BIIGLE, allowing other modules to extend yours.