Images from the deep Coral Sea
Dhugal Lindsay, Country Leader for Japan, recently took part in the Schmidt Ocean Institute-sponsored cruise “Seamounts, canyons and reefs of the Coral Sea” via telepresence in order to collect images of gelatinous macroplankton for the wwwPIC project. In the coming months, taxonomically-vetted images of various species will be harvested from the original high quality video footage to help train a machine learning model to recognize the species in Remotely-Operated Vehicle (ROV) footage. The dives, which were live-streamed on YouTube, can be found, with Lindsay’s commentary, at the following links:
ROV Dive 373 - Coral Sea Marine Park - Cairns Seamount (Streamed live on 6 Aug 2020)
ROV Dive 376 - Coral Sea Marine Park - Herald Cays (8 Aug 2020)
ROV Dive 377 - Coral Sea Marine Park - Malay Reef (10 Aug 2020)
ROV Dive 389 - Coral Sea Marine Park - Osprey Reef (21 Aug 2020)
ROV Dive 392 - Coral Sea Marine Park - Tregrosse Reefs (25 Aug 2020)
New imaging sensor integrated on a glider
Marc Picheral, engineer in Villefranche (France), supervised the integration of the UVP6 imaging sensor that he invented on the SeaExplorer glider from ALSEAMAR. The glider carried out a full back and forth transect across the Ligurian current and the UVP6 worked nominally. This test deployment revealed hiccups with other sensors (that is what tests are for afterall!) but, on the plankton imaging side, we are ready to deploy this platform next spring. The glider equipped with the UVP6 will generate a large number of images which will be processed and integrated into EcoTaxa. This data will serve as a demonstration of the use of the infrastructure in the last years of the project, as part of Thelma Panaïotis' PhD thesis.
EMODnet Biology Workshop
Laurent Salinas, the developer working on EcoTaxa for WWWPIC, followed the EMODnet Biology (all online...) workshop, to learn more about how to send data from EcoTaxa to EMODnet and then OBIS. After these two weeks, a first implementation of an export format for EMODnet is ready and passes the first quality tests. Now we "just" need to make it bullet proof ;-)
A comprehensive learning set for the ISIIS instrument
Moritz Schmid, who works as a post doc on the project, prepared an extensive data of ISIIS images from the Northern California Current and uploaded it on EcoTaxa. With ~83,000 images distributed alsmost evently in 170 classes, it will allow to test various classification techniques and bootstrap the creation of other datasets for the same instrument.
IFB will host EcoTaxa-EU
The French Institute of Bioinformatics is a national infrastructure dedicated to storing and computing with biological data, primarily nucleic acid sequences. Quantitative images, that are the target of WWWPIC, are small and numerous and the technical requirements to store and process them are close to those for nucleic acids sequences.
After examining the requirements, IFB has agreed to host an instance of EcoTaxa to serve as the European node of the WWWPIC infrastructure. In the meantime, the code is being adapted for running on such professional hosting services, by modularising it and packaging it into Docker containers. This will help its deployment in other countries.
EcoTaxa in Chinese
As part of the wider collaboration network around WWWPIC, our collaborators from the company Watertools in China have deployed an instance of EcoTaxa and translated most of its interface in Chinese. We will continue to work towards easing such internationalisation by separating the code and the messages in the user interface, but it already looks very cool with Chinese characters!
We will also work with Watertools and the Institute of Oceanology of Chinese Academy of Sciences to find a good hosting place for this instance and integrate it in the network of EcoTaxa nodes that WWWPIC is building.
Intern Adeb Zaoui started working remotely because of the current sanitary crisis. Under the supervision of Éric Debreuve and Cédric Dubois, he has explored a hierarchical image classification deep neural network on a standard dataset. He was able to reproduce the results of a recent paper on the topic. Now, he will be moving to plankton images.
UniEuk + WoRMS
The UniEuk project provides the current taxonomic backbone of the EcoTaxa application, which is one of the the main tools in the WWWPIC project. Having a reliable, universal taxonomy is the starting point for any ecological dataset.
To be able to provide such datasets to other databases, they need to share a common taxonomy. Uploading datasets to OBIS is one important objective of WWWPIC and OBIS uses the well-known WoRMS taxonomy. UniEuk has recently integrated the WoRMS taxonomy, to complete its coverage and so that individual taxa identifiers can be translated from one convention to the other. This is an important first step towards sending data to OBIS!
Reference image datasets
One goal of WWWPIC is to provide reference datasets of curated images to train new machine learning models. We started with a dataset of 72k images for the ISIIS instrument. It is currently being complemented by two other datasets for the same instrument but where each organism has been carefully segmented manually and a larger, more diverse dataset from the Northern California Current being prepared now.
Beyond ISIIS, we improved upon a reference dataset for the ZooScan instrument, that currently holds 1.4M images sorted in ~160 classes, and are currently building a new one for the FlowCam instrument.
New participant to WWWPIC
Rainer Kiko, a long time collaborator of the plankton team at Laboratoire d'Océanographie de Villefranche (LOV) got awarded a prestigious Make Our Planet Great Again grant from the French government (he is pictured here during a reception for the program at the Elysée presidential palace in Paris). This will fund him for five years to work in Villefranche and we are very happy to welcome him to the team.
Given his involment in all things "imaging", we already invited Rainer and his PhD student, Martin Schroeder, to the WWWPIC kickoff meeting in Paris. But now that Rainer is a French government employee, he can formally be part of WWWPIC!
New plankton image datasets
We hired Louis Caray-Counil to sort images from the ISIIS instrument that were prepared by Thelma Panaïotis, a PhD student working on the project. This will enrich the collection of datasets hosted on EcoTaxa, one of the infrastructures that will be developed through WWWPIC. Louis sorted a dataset of ~72k images that will serve as a reference for the future classification of images from this instrument. Together with Thelma, they also laid the ground work to evaluate our image segmentation algorithms by carefully outlining known organisms on the original images from ISIIS.
This work highlighted some planktonic beauties like the delicate Physonect siphonophore displayed here.
On July 8th and 9th we met at the Agence Nationale de la Recherche building in Paris with the two other laureates of the Belmont Forum SEI CRA call, to present our projects and think towards future interactions. It was a good opportunity for the WWWPIC to meet for the first time in person as well as to get to know the principal investigators of the other projects. There even was an exhibition of plankton photographs in the Jardin des Plantes (see picture), a good omen.
Then we sayed in Paris for an additional day and a half to meet with other WWWPIC partners and plan the more technical aspects of the project. Members of OBIS, UniEuk, EMODNET biology, and IFB were present, as well as external partners from GEOMAR Helmholtz Centre for Ocean Research. It was a very productive time and many plans were outlined. Now we need to carry them out!