×

Manual

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.

Account settings

Learn how you can manage your user account.

Notifications

View and manage BIIGLE notifications in the notification center.

Projects

Learn what projects are and how to manage them.

Label Trees

About Label Trees

Learn what label trees are and how you can manage them.

Manage Labels

Learn how to create, modify or delete labels of a label tree.

Label Tree Versions

Everything you need to know about versioned label trees.

Merge Label Trees

View and resolve differences between label trees.

Annotation Catalog

The annotation catalog shows you all annotations with a certain label.

Download and import

Learn more on how you can download a label tree and use it elsewhere.

Volumes

Volume overview

The volume overview allows you to explore all images that belong to a volume.

Remote volumes

With remote volumes you can use images from your own data source in BIIGLE.

Annotation sessions

Annotation sessions can be used to conduct scientific studies.

Image metadata

Upload image metadata to add information that can't be extracted from the images.

Image Labels

Image labels are labels that are attached to whole images.

Annotations

Getting Started

A quick introduction to the annotation tool.

Creating Annotations

Learn about all the tools that are available to create new annotations.

Editing Annotations

Learn about all the tools to modify or delete existing annotations.

Navigating Images

Learn about advanced ways to navigate the images in the annotation tool.

Sidebar

All sidebar tabs of the annotation tool explained.

Shortcuts

A list of all available shortcut keys in the annotation tool.

URL Parameters

Advanced configuration of the annotation tool.

Largo

The Label Review Grid Overview and what you can do with it.

Reports schema

A description of the file formats of the different available reports.

Volume map

The volume map shows the locations of images on a world map.

Laser point detection

The automatic laser point detection is used to determine the visual footprint of images.

Annotation assistance requests

Learn how to ask any person for advice on the label of an annotation.

MAIA

About MAIA

An introduction to the Machine Learning Assisted Image Annotation method (MAIA).

Novelty detection

A description of the first MAIA stage and the configurable parameters.

Training proposals

A description of the second MAIA stage.

Instance segmentation

A description of the third MAIA stage and the configurable parameters.

Annotation candidates

A description of the last MAIA stage.

Video Annotations

Getting Started

An introduction to the video annotation tool.

Creating Video Annotations

Learn how to create different kinds of video annotations.

Navigating the Timeline

Learn about the video timeline and how to navigate it.

Editing Video Annotations

Learn about all the tools to modify or delete existing video annotations.

Sidebar

All sidebar tabs of the video annotation tool explained.

Shortcuts

A list of all available shortcut keys in the video annotation tool.

URL Parameters

Advanced configuration of the video annotation tool.

Remote Videos

With remote videos you can use videos from your own data source in BIIGLE.

References

Reference publications that you should cite if you use BIIGLE for one of your studies.

BIIGLE 2.0
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: 10.3389/fmars.2017.00083

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: 10.3389/fmars.2015.00020

MAIA
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: 10.1371/journal.pone.0207498

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: 10.1109/CVPR.2017.515

Developer Documentation

RESTful API

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.

RESTful API documentation

Server

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.

Server API documentation

Developer Tutorials

Package development

Learn about PHP package development and how to add custom functionality to your BIIGLE installation by developing your own modules.

Advanced package development

Learn how to add new views and routes with a custom package and how to properly test them using the BIIGLE testing environment.

Using custom assets in packages

Learn how to handle custom assets like CSS and JavaScript in addition to the defaults provided by the core application.

Mastering view mixins

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.