Biology

Amplify the impact of marine research imagery using Marimba, an open source Python framework

Chris Jackett unveiled the marimba in front of scientists and engineers from around the world at the recent Marine Imaging Workshop 2024. Credit: Alan Williams/CSIRO

It’s not always easy to see the big picture when you’re deeply immersed in a project. Innovation often requires taking a step back to assess how the impact of science can actually be amplified.

Chris Jackett and his colleagues at the Sustainable Ocean Futures Program focus on advancing marine biodiversity research. They collect and process extensive marine image datasets. Their desire to maximize the impact of their discoveries and improve accessibility for the scientific community led to the creation of Marimba.

A symphony of efficiency and collaboration

Marimba is a Python framework designed in collaboration with Monterey Bay Aquarium Research Institute (MBARI). Streamline the structuring, management, and processing of scientific imaging datasets while adhering to globally recognized FAIR principles. These are a set of standards that aim to make data “searchable, accessible, interoperable, and reusable.”

“Finding, accessing and using ocean imagery in a vast ocean of scientific data has long been a challenge for researchers around the world,” Jackett said.

“Complexed by diverse data formats, rapidly increasing image volumes, and inconsistent workflows. We didn’t have a system, so we built one.”

Main functions of marimba and their influence

“Marimba is useful for anyone involved in science who manipulates images and derives data from them,” Jackett said.

“It doesn’t matter where the image comes from, whether it’s a Canon DSLR or a GoPro system. It can also be used with more specialized equipment like an imaging flow cytometer.”

The marimba is designed to meet three main needs.

standardization

It provides a standardized structure and context for managing the entire FAIR image dataset workflow, including import, processing, packaging, and distribution.

flexibility

Marimba is highly customizable and adapts to the diverse requirements of different imaging equipment used in scientific research.

process

Automate common repetitive tasks while providing access to powerful built-in image processing capabilities to significantly accelerate research workflows.

Global launch of marimba

Jackett recently presented the marimba’s capabilities to an audience of scientists and engineers from around the world at the 5th Marine Imaging Workshop 2024.

“This launch is an important milestone for Marimba, providing researchers with powerful tools to enhance their research and collaborate more effectively,” Jackett said.

“This has the potential to change the way we understand and protect our oceans, with the potential to unlock deeper insights, accelerate research and drive future marine conservation and resource management strategies. It allows us to promote international cooperation.

“By designing the marimba as an open-source tool, CSIRO ensures that the marimba can be continuously grown, improved and used by scientists across a variety of research fields, extending its impact.

“This is a different kind of impact than publishing a scientific paper in a high-impact journal, but developing these innovative solutions is important for researchers both at CSIRO and the wider scientific community. It’s important.”

Citation: Amplifying the Impact of Marine Research Imagery with Marimba, an Open Source Python Framework (November 1, 2024), from https://phys.org/news/2024-11-amplifying-impact-marine-imagery Retrieved November 1, 2024-marimba.html

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