Explained: new ways to peer deep under our oceans

Marine and ocean researchers in Australia and the US have developed an innovative open-source framework which they say transforms how research image datasets are managed, processed and shared, setting a new standard for scientific collaboration, citizen science and data accessibility.

The work builds on various projects which are opening up the underwater world for scientists and the general public, including the Integrated Marine Observing System (IMOS) and what’s known as UMI – Understanding of Marine Imagery project.

Although these are science endeavours, the data projects are all open source and millions of the images are available to the marine-curious public.

For example one of these projects is “Marimba,” which required Australia’s national science agency, CSIRO and a team at the Monterey Bay Aquarium Research Institute (MBARI) in California, to collaborate for more than a year to create the open-source tool.

When processing images taken hundreds of meters below the water surface, using Marimba, geotags are added to the images, so they can be displayed in Google Earth, or they can be harvested into online platforms such as Seamap Australia and SQUIDLE+. There they can be made accessible to the public and scientists for viewing and further research.

“The ‘explore map’ feature of SQUIDLE+ is one of the ways we can access and explore images described and packaged by the new tool, Marimba,” says Franzis Althaus from the CSIRO in Hobart who manages deep-sea image data sets.

“At this stage only one deep-sea data set from an expedition to seamounts (underwater mountains) south of Tasmania is available in SQUIDLE+. Marimba will help us package and publish many more such data sets.”

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Breakout: How a researcher found the first deep-sea skate nursery in the Southern hemisphere.

Researcher Kylie Maguire from the CSIRO Environment used the images from a voyage to a seamount off southern Tasmania and discovered an egg nursery for the skate Amblyraja hyperborea  which is a chondrichthyan (sharks, skates, rays and chimaeras), a group in global decline.

Maguire’s research paper says, off Australia, coral reef egg case nursery habitat is restricted to a narrow depth range in temperate latitudes where it is scarce and impacted by historical bottom trawl fishing in many locations.

To follow how Maguire found this nursery, the metadata created by the Marimba project is very helpful.

Click on the map at the top of this article, which will take you to “SQUIDLE+ Explore” page.

On the right hand side in the “Explore” column, click on the “Filter view by platform” box and select “CSIRO O&A MRITC Towed Stereo Camera.”

If you click on the dot that appears in the centre of the page, you will see there were 123 deployments of a CSIRO towed underwater camera creating 130,876 media items, over 23 days!

Back on the right hand column, under the next drop box “Select Deployment” click on the left arrow which will display “IN2018_VO6″. Click on that number and a long list of new numbers appears alongside a map of Tasmania.

Scroll down that list and select “IN2018_V06_098” which will then be displayed under the “Selected deployments” heading on the Explore column. Click the deployment name at the head of the column. It will drop down a list of available images and a map of Tasmania.

Next, in the black “EXPLORE” bar at the top of the map select the Media tab. It will open some of the images.

Use the scroll bar on the far right, scroll down to #109.

This image was taken at 1294m depth it shows a reef formed by the stony coral Solenosmilia variabilis that forms the habitat for other corals, urchins and sponges. In this image Maguire had noticed the skate eggs distributed throughout the coral matrix. That led to identifying the area as a nursery habitat for a deep-sea skate.

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Chris Jackett from the Sustainable Marine Futures program at CSIRO says Marimba is a Python framework designed in collaboration with the MBARI.

“It streamlines the structuring, managing and processing of scientific image datasets while adhering to the globally recognised FAIR principles. (The FAIR principles are a set of standards that intend to make data Findable, Accessible, Interoperable and Reusable.) 

“In the vast ocean of scientific data, finding, accessing, and utilising marine imagery has long been a challenge for researchers worldwide, compounded by diverse data formats, rapidly increasing volumes of imagery, and inconsistent workflows,” says Jackett.

“Since there wasn’t a system available that could efficiently process and package our scientific marine image datasets while adhering to FAIR principles – we built one.”

Jackett unveiled Marimba to a global audience of scientists and engineers at the recent Marine Imaging Workshop 2024.

“Marimba can help anyone involved in science working with imagery and deriving data from it.

“It doesn’t matter where the imagery is sourced from – whether it’s from a Canon DSLR or a GoPro system. It can even be used for more specialised instruments like imaging flow cytometers.

“It holds the potential to transform how we understand and protect our oceans- allowing us to extract deeper insights, accelerate research and foster international collaboration that could drive future marine conservation and resource management strategies.”

The images give users an understanding of what’s on the seafloor, a place they can never visit. Captured in the image are low-profile reef systems in north west Tasmania, smothered in sandy sediment. Growing out of these reefs are brightly coloured sponges, small gorgonian fans and soft fluffy bryozoans.

Jacquomo Monk, a senior marine ecologist at the Institute for Marine and Antarctic Studies at the University of Tasmania is refining underwater imagery methods to generate essential data for informed management of marine ecosystems.

Jac’s work spans remarkable underwater landscapes, from the dark, frigid depths of southern Tasmania to the warm, clear waters of St. Lucia. He is the lead scientist for initiatives like SQUIDLE+ and Seamap Australia, where his contributions have significantly advanced the establishment of a national monitoring system for Australian Marine Parks.

“This image was collected in 107m in the Zeehan Marine Park (west of King Island) as part of a project funded by Parks Australia to map the park,” Monk told Cosmos.

“Thanks to platforms like SQUIDLE+, these images and annotations were then re-used in a national project funded through the NESP Marine and Coastal Hub to enhance the capacity of Australian Marine Park managers to protect natural values and assess the effectiveness of management in the South-west and South-east Marine Park Networks.”

“Final mapping products are hosted by Seamap Australia, enabling the dynamic exploration of model predictions, composition of ground-truthing observations represented as spatially-referenced pie charts, and links back to the habitat images hosted through SQUIDLE+. Visit this site to access these features.

This image above is just one of the nearly 10 million fully openly accessible images of the seafloor hosted in SQUIDLE+.

Ariell Friedman, the chief software architect and principal developer of SQUIDLE+, says since SQUIDLE+ started in mid-2020, it has established itself as the most comprehensive and mature end-to-end platform globally with nearly 10 million fully openly accessible images.

“SQUIDLE+ has imagery covering both Poles and everything in between from 26 distinct data sources,” Friedman says.

Here’s another image from the Zeehan data set taken at 101m.

Another way to explore the oceans without getting wet.