Software

Marimba: Open Source Software Repository for FAIR Scientific Image Data Management

Commonwealth Scientific and Industrial Research Organisation
Jackett, Chris ; Barnard, Kevin ; Mortimer, Nicolas ; Webb, David ; Althaus, Franzis ; Tyndall, Aaron ; Untiedt, Candice ; Devine, Carlie ; Gorton, Bec ; Scoulding, Ben
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ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rfr_id=info%3Asid%2FANDS&rft_id=http://hdl.handle.net/102.100.100/661195?index=1&rft.title=Marimba: Open Source Software Repository for FAIR Scientific Image Data Management&rft.identifier=http://hdl.handle.net/102.100.100/661195?index=1&rft.publisher=Commonwealth Scientific and Industrial Research Organisation&rft.description=Marimba is an open-source Python framework designed for researchers, data scientists, and engineers to help structure, process, package and distribute FAIR (Findable, Accessible, Interoperable, and Reusable) scientific image datasets. The framework provides comprehensive functionality for managing the entire workflow of scientific image data processing, from post-acquisition data importing through to final dataset packaging and distribution. Marimba includes built-in support for parallel processing, file hard linking to optimise storage usage, and integration with the iFDO (image FAIR Digital Object) metadata standard. The framework is well documented and comes with four operational Pipeline examples that demonstrate its use across different applications: Zeiss Axio microscopy, FlowCam plankton imagery, deep-sea towed camera surveys, and historical image digitisation. While initially developed for marine science applications, Marimba's modular design makes it adaptable for any field dealing with scientific imagery.\nLineage: Marimba was conceptualised at CSIRO in late 2022, with substantial elements of its initial design and implementation developed during the CSIRO Image Data Collection and Delivery Hackathon in early 2023. Further collaborative development between CSIRO and MBARI occurred in late 2023. The framework was open-sourced on GitHub and published as a Python package on PyPI in mid-2024, and officially launched at the Marine Imaging Workshop in late 2024. The development process involved extensive collaboration between software engineers, marine scientists, and data managers to ensure robust functionality and adherence to FAIR data principles.&rft.creator=Jackett, Chris &rft.creator=Barnard, Kevin &rft.creator=Mortimer, Nicolas &rft.creator=Webb, David &rft.creator=Althaus, Franzis &rft.creator=Tyndall, Aaron &rft.creator=Untiedt, Candice &rft.creator=Devine, Carlie &rft.creator=Gorton, Bec &rft.creator=Scoulding, Ben &rft.date=2025&rft.edition=v1&rft_rights=CSIRO Binary Software Licence https://research.csiro.au/dap/licences/csiro-binary-software-licence-agreement/&rft_rights=Data is accessible online and may be reused in accordance with licence conditions&rft_rights=All Rights (including copyright) CSIRO 2024.&rft_subject=Python framework&rft_subject=FAIR data principles&rft_subject=scientific imaging&rft_subject=marine science&rft_subject=image processing&rft_subject=data management&rft_subject=open source software&rft_subject=underwater imagery&rft_subject=data packaging&rft_subject=automation&rft_subject=parallel processing&rft_subject=research software&rft_subject=marine imaging&rft_subject=data standardisation&rft_subject=scientific workflows&rft_subject=Data management and data science not elsewhere classified&rft_subject=Data management and data science&rft_subject=INFORMATION AND COMPUTING SCIENCES&rft_subject=Software engineering not elsewhere classified&rft_subject=Software engineering&rft.type=Computer Program&rft.language=English Access the software
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https://research.csiro.au/dap/licences/csiro-binary-software-licence-agreement/

Data is accessible online and may be reused in accordance with licence conditions

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Marimba is an open-source Python framework designed for researchers, data scientists, and engineers to help structure, process, package and distribute FAIR (Findable, Accessible, Interoperable, and Reusable) scientific image datasets. The framework provides comprehensive functionality for managing the entire workflow of scientific image data processing, from post-acquisition data importing through to final dataset packaging and distribution. Marimba includes built-in support for parallel processing, file hard linking to optimise storage usage, and integration with the iFDO (image FAIR Digital Object) metadata standard. The framework is well documented and comes with four operational Pipeline examples that demonstrate its use across different applications: Zeiss Axio microscopy, FlowCam plankton imagery, deep-sea towed camera surveys, and historical image digitisation. While initially developed for marine science applications, Marimba's modular design makes it adaptable for any field dealing with scientific imagery.
Lineage: Marimba was conceptualised at CSIRO in late 2022, with substantial elements of its initial design and implementation developed during the CSIRO Image Data Collection and Delivery Hackathon in early 2023. Further collaborative development between CSIRO and MBARI occurred in late 2023. The framework was open-sourced on GitHub and published as a Python package on PyPI in mid-2024, and officially launched at the Marine Imaging Workshop in late 2024. The development process involved extensive collaboration between software engineers, marine scientists, and data managers to ensure robust functionality and adherence to FAIR data principles.

Available: 2025-02-25

Data time period: 2022-12-01 to ..

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Data Management and Data Science | Data Management and Data Science Not Elsewhere Classified | FAIR data principles | Information and Computing Sciences | Python framework | Software Engineering | Software Engineering Not Elsewhere Classified | automation | data management | data packaging | data standardisation | image processing | marine imaging | marine science | open source software | parallel processing | research software | scientific imaging | scientific workflows | underwater imagery |

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