Amplifying the impact of research imagery with Marimba
A newly designed, innovative open-source framework will transform how research image datasets are managed, processed and shared – all while following the FAIR principles.
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By
Gail Burke1 November 20242 min read
Key points
Our researchers have developed Marimba, an open-source Python framework to streamline the processing of scientific image datasets.
Developed collaboratively by CSIRO and MBARI, it offers a comprehensive solution for managing, processing, and packaging image data.
An open-source release empowers global scientific collaboration, helping researchers find, access, and use imaging data more efficiently.
It’s not always easy to see the big picture when deeply immersed in a project. Innovation often requires stepping back to assess how we can really amplify the impact of our science.
Chris Jackett and his colleagues in the Sustainable Marine Futures program focus on advancing marine biodiversity research. They collect and process extensive marine image datasets. Their desire to maximise the impact of their findings and improve accessibility for the scientific community led them to create Marimba.
CSIRO and MBARI researchers collaborated for more than a year to create the open-source tool Marimba.
Symphony of efficiency and collaboration
Marimba is a Python framework designed in collaboration with the Monterey Bay Aquarium Research Institute (MBARI). It streamlines the structuring, managing and processing of scientific image datasets while adhering to the globally recognised FAIR principles. These 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," Chris said.
"Compounded by diverse data formats, rapidly increasing volumes of imagery, and inconsistent workflows. 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."
"Marimba can help anyone involved in science working with imagery and deriving data from it," Chris said.
"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."
Marimba has been designed to meet three core needs.
Standardisation
It provides a standardised structure and context for managing the entire workflow of FAIR image datasets, including importing, processing, packaging, and distribution.
Flexibility
Marimba is highly customisable, adapting to the diverse requirements of various imaging instruments used in scientific research.
Processing
It automates common and repetitive tasks while providing access to powerful built-in image processing features, significantly accelerating research workflows.
Marimba's global launch
Chris recently unveiled the capabilities of Marimba to a global audience of scientists and engineers at the 5th Marine Imaging Workshop 2024.
"The launch marks a significant milestone for Marimba, offering researchers a powerful tool to enhance their work and collaborate more effectively," Chris said.
"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.
"By designing Marimba as an open-source tool, CSIRO ensures that it can continue to grow, improve, and potentially be used by scientists in many different fields of research – and magnify its impact.
"It's a different type of impact than publishing a scientific paper in a high-impact journal, but developing these innovative solutions is critical for researchers both within CSIRO and the broader scientific community."
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