EcoTaxa is a web application destined to process the large number of images generated by such quantitative imaging instruments. It leverages deep learning and an efficient user interface to allow taxonomists to classify thousands of images per day. In addition, it can store a large quantity of metadata together with the images, with very few constraints on its content. These metadata can be used by the operators to sort through the images and by the machine learning backend to suggest identifications. Finally, EcoTaxa can export the metadata and the identifications together, in a versatile text table or following the DarwinCore Archive standard, for further data exploitation.
This is the backend part of the application, which is coupled with a front-end.
In docker you can find build scripts, as well as a simple docker-compose configuration for setting up a server quickly, without impacting your whole system. It also embeds a PgAdmin4 docker image.
The simplest way to set up a running instance is to follow the all_in_one instructions. This will give you a solution but probably not scale to be a production environment.
In this directory:
pyis for Python back-endQAcontains all tests & measurements on the code.
The UI itself is a server-side Flask app, in the ../ecotaxa folder.
The image vault is shared between this back-end and the front-end.
The back-end reads the config.cfg file from the front end and derives from there.
To launch the docker DB server:
cd dockerdocker-compose up
More detailed instructions are in the documentation
If you use EcoTaxa in your work, please cite it as
Marc Picheral, Sébastien Colin, and Jean-Olivier Irisson (2017) EcoTaxa, a tool for the taxonomic classification of images. http://ecotaxa.obs-vlfr.fr
This code is released under the GPLv3.
Specifications and supervision
- March Picheral, Laboratoire d'Océanographie de Villefranche (LOV), CNRS 0000-0001-8172-5473
- Jean-Olivier Irisson, Laboratoire d'Océanographie de Villefranche (LOV), Sorbonne Université 0000-0003-4920-3880
Current developers
- Béatrice Caraveo, Laboratoire d'Océanographie de Villefranche (LOV), Sorbonne Université
- Laurent Salinas, DevInitIf (previously Laboratoire d'Océanographie de Villefranche (LOV), Sorbonne Université)
- Julie Coustenoble, Laboratoire d'Océanographie de Villefranche (LOV), Sorbonne Université
Past contributors
- Sebastien Colin, Station Biologique de Roscoff, Sorbonne Université
- Laurent Navarro, AltiDev
- Laurent Reese, Laboratoire d'Océanographie de Villefranche (LOV), Sorbonne Université