Marjolijn Christianen - Marine Ecology Research

Automated detection of vegetation and megaherbivores from drone imagery using deep learning – New paper

Does deep learning and coding deter you from using it? As ecologists, we experienced that too, but we have dived in. In our new paper, led by Rebecca James, we employed deep learning to automate the analysis of aerial drone imagery to assess spatial patterns within subtidal #seagrass meadows and the distribution of turtles UNDERWATER 🌊🐢.

Now you can try deep learning on your own system because we provide accessible, open-access tools to automatically classify vegetation and animals in aerial imagery.

🌿🚁 Paper highlights:
* Deep learning efficiently detected subtidal seagrass patterns and sea turtle distribution at large scales.
* By comparing over space and time, we were able to identify changes in the spatial patterning of seagrass patterns and used this to infer the resilience of the meadow.
* Comparing 2012 vs. 2022 data demonstrates the adaptability of deep learning models for retraining with new aerial imagery.
* Lower ecosystem resilience was observed at meadow edges, with resilience declining over a decade.
* These new tools provide a quantitative method for monitoring ecosystems and inferring resilience. And stimulate the uptake of deep learning for ecological applications.

Read the paper here: https://doi.org/10.1016/j.ecoinf.2024.102580“Monitoring vegetation patterns and their drivers to infer resilience: Automated detection of vegetation and megaherbivores from drone imagery using deep learning”

The deep learning and post-processing scripts can be found here

https://git.wur.nl/deep-learning-tools615for-marine-ecosystem-monitoring
📝 Authors: Lead and scientific millipede; Rebecca James, Machine learning champions; hashtag#Freek Daniels, Aneesh Chauhan, Remote sensing experts; Pramaditya Wicaksono, Muhammad Hafizt, and Setiawan Djody Harahap; and myself thanks to hashtag#NWO-WOTRO for the funding
hashtag#DroneMagic hashtag#DeepLearningDiscoveries hashtag#TeamScience hashtag#NewPublication 🌱🔍🚀

*To examine vegetation patchiness and infer resilience the vegetation patch density is*
*plotted against the vegetation patch size for each subset image (representing an area of 12 x 16* *m) in the 2012 (black circles) and 2022 (green triangles) aerial imagery. The physical upper limit* *of the patch density versus patch size is depicted with the dashed red line. Patchiness increases* *with a decline in patch size and density, with the distance of the points from the physical limit* *providing an indicator of the resilience i.e. the further the distance, the lower the resilience.* *Numbered images of vegetation patchiness above display the region that the corresponding* *numbered point represents. Graph inset displays all of the points with a patch size proportion* *between 0 and 0.1 of 10 m2.*

Concerns over record ocean water temperatures: ‘No time for ecosystem recovery’

‘World’s average ocean surface temperature measured 21.1 beating the previous high of 21C set in 2016’. As a scientist, I was asked to explain to national news (NOS Saturday evening news) the impact of rising temperatures and the resulting frequency of marine heat waves on ecosystems, together with Erik van Sebille.

Field trip and workshop to map Indonesian seagrass resilience

Time to go back to Indonesia. A short report on the field trip and workshop:

Why seagrass needs space – a long read on the 1st world seagrass day

🌊 #Longread – Despite the many threats, seagrass habitats still have the potential to store large amounts of carbon and restore the balance of the sea. On 1 March 2023 – the very first World Seagrass day – we explain why we need to protect and rewild the sea, and share how camera-equipped sea turtles and tiger sharks can help us do it:

#Rewilding, #Seagrass, #ClimateChange, #Biodiversity

Do you see the “S” of “seagrass” planted in the sand?

Last week we (Karin Didderen, Fee Smulders, and I) were invited to the seagrass restoration week in #bonaire ! We started a new seagrass restoration site in Lac Bay as part of the Lac Pa Semper – RESEMBID project (https://stinapabonaire.org/nature-projects/lac-pa-semper/), coordinated by Jessica Johnson. Most inspiring was the training of

Seagrass ecosystem multifunctionality under the rise of a flagship marine megaherbivore

How does ecosystem functioning change now megaherbivores are returning? In our new paper today in Global Change Biology we show that the return of the green turtle has strong effects on seagrass ecosystem functions and can even reduce multifunctionality with ~25%. Read the short & simple summary below.

Documentary ‘Leatherback’

— Update, Sept 2022 — The documentary won the “Gouden Hert” competition 2022 at the International Short Films Festival in Arnhem.

In 2021 I was happy to be involved in the making of a documentary with Artist Mirthe Dokter, together with Rian van den Boom and others.

This unconventional docu shows an intriguing portrait of the leatherback sea turtle, threatened with extinction. In Ghana, artist Mirthe meets ‘Uncle Raf’, the leader of a turtle conservationists team in a small fishing town. Slowly, she gets entangled in the web of all the difficulties that come with protecting this ancient animal. Virtual artists Mirthe records her story in a painted diary, that she shares with a marine ecologist, Marjolijn, from the Netherlands.

Restoring Bonaire’s seagrasses and mangroves a checkerboard at a time

Seagrass and Mangroves on Bonaire can use a helping hand. Water quality, tourists (trampling), Sargassum tides and more, have caused rapid decline of seagrasses and mangroves. Based on results from an earlier pilot, last week we launched a larger scale seagrass restoration project to help counter this decline. And also set up pilots to test the use of a new method for mangrove restoration alongside other ongoing methods. We used biodegradable mats that need only a little amount of donor material. The structure of these mats stabilize the sediment for the young plants to facilitate settlement, mimicking the natural effect of nature root mats.

Fish can protect ecosystems from invasive seagrass

One grazer is not like another. Where sea turtle grazing gives way to invasive eelgrass, fish grazing has the opposite effect. “Protected areas with abundant native grazing fish may be more resistant to expansion of invasive eelgrass.

Savannas of the sea: “Pristine seagrass meadows were often heavily grazed”

WUR press release:

Seagrasses are important for our coastal protection, biodiversity and carbon sequestration. But contrary to popular belief, dense, waving seagrass meadows with long foliage are not necessarily more natural. In a new publication in Nature Ecology & Evolution, researchers from Wageningen University & Research and Radboud University argue for a more nuanced picture of natural seagrass meadows being dense vegetation interspersed with areas grazed by sea turtles. This calls for a change in our nature management practices.