LEAF: Lightweight equipment adapter framework

List of Authors

  1. Matthew Crowther
    ,  
  2. Brett Metcalfe
    ,  
  3. Carlos Suarez
    ,  
  4. David Camilo Corrales ,  
  5. Jairo Alexander Astudillo Lagos
    ,  
  6. Anil Wipat
    ,  
  7. Timothy J. Rudge
    ,  
  8. Katherine James ,  
  9. Jasper J. Koehorst
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Abstract

Background

As our understanding of complex (biological) systems within the (life) sciences increases, so does the continuous demand for data to maintain that understanding. New approaches for knowledge generation, real-time prediction, and decision-making, such as machine learning, do not reduce this data deficit, instead requiring diverse and continuously updated data streams. Furthermore, in order to be reusable, machine-readable and computationally tractable, such diverse datasets must be seamlessly integrated and efficiently processed across different sources, necessitating a form of standardization. However, the amount and diversity of data required far exceed the capabilities of capturing and curating data manually, making manual approaches increasingly infeasible. One solution would be the automation of, or at least enhancement of, digitization of research data. Although automation of research environments and automated data extraction are not new ideas, the issue of vendor-specific software, processes, and data structures makes generic inter-equipment data extraction challenging. A “one-size-fits-all” approach can be difficult with such diverse and disparate systems. Results Here, the Lightweight Equipment Adapter Framework (LEAF) is introduced, a modular open-source system that can be adapted to monitor different equipment and extract data automatically. LEAF is flexible and scalable, enabling integration with various types of communication protocols, instruments, and data formats. By leveraging reusable modules, the framework allows for rapid development of new adapters, minimizing the effort required to support additional equipment. Once deployed, LEAF operates with minimal human intervention, facilitating continuous and automated data collection. Standardisation of data is achieved through automated data collection, ensuring interoperability across different systems and enabling more efficient data analysis and downstream processing.

Conclusions

LEAF shifts compliance with data standards to the instrument level, generating better metadata, and allowing the integration of data from diverse sources. Ultimately, LEAF addresses the challenge of fragmented laboratory and research automation by providing a unified, adaptable solution for extracting and structuring experimental data.

Plain Language Summary

Research often heavily depends on vast quantities of data generated by many different and diverse laboratory instruments and systems. At the same time, technologies such as artificial intelligence and machine learning require continuous, well-structured, and reusable data streams. However, research equipment from different manufacturers often stores data in incompatible formats, making it difficult to combine and analyze information efficiently. As datasets grow the manual collection and curation of these datasets is becoming increasingly impractical.

To address this challenge, we developed the Lightweight Equipment Adapter Framework (LEAF), an open-source system that automatically connects to equipment and extracts data. LEAF is flexible and modular, allowing it to work with many types of instruments, communication protocols, and data formats. New adapters can be added with limited effort, making the system scalable and reusable.

By automating data collection and standardization, LEAF improves interoperability, reduces manual workload, and supports more efficient analysis and integration of research data across diverse systems.

Corresponding author
Brett Metcalfe
Grant information

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 101094287 (RI services to promote deep digitalization of Industrial Biotechnology – towards smart biomanufacturing [BIOINDUSTRY 4.0]). J.J.K acknowledges the Dutch Research Council (NWO) and Wageningen University & Research for their financial contribution to the UNLOCK initiative (NWO: 184.035.007). LEAF is funded by the Dutch Research Council (NWO) and Open Science NL under grant agreement No. 500.040.2488 (Transforming Research Equipment Connectivity: An Open IoT Platform for Real-Time Data Collection and Digital Twinning). C.S. was funded through Call 823 – High-Level Training of Human Capital for the Cauca region. C.S. and D.C.C. acknowledge the support of the Ministry of Science, Technology, and Innovation (MinCiencias).

The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Copyright
© 2026 Matthew Crowther (Co-Author); Brett Metcalfe (Corresponding Author, Co-Author); Carlos Suarez (Co-Author); David Camilo Corrales (Co-Author); Jairo Alexander Astudillo Lagos (Co-Author); Anil Wipat (Co-Author); Timothy J. Rudge (Co-Author); Katherine James (Co-Author); Jasper J. Koehorst (Co-Author) Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 International License.

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Authors & roles

Matthew Crowther

Newcastle University, Newcastle upon Tyne, England, UK

Roles
Co-Author, Conceptualization, Formal Analysis, Investigation, Methodology, Software, Validation, Writing – Original Draft Preparation

Brett Metcalfe

Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Gelderland, The Netherlands

Roles
Corresponding Author, Co-Author, Conceptualization, Formal Analysis, Funding Acquisition, Project Administration, Software, Supervision, Validation, Writing – Original Draft Preparation, Writing – Review & Editing

Carlos Suarez

Departamento de Telemática, Universidad del Cauca, Popayán, Colombia

Roles
Co-Author, Methodology, Software, Validation

David Camilo Corrales

CNRS, INRAE, INSA, Université de Toulouse, Toulouse, France

Roles
Co-Author, Conceptualization, Supervision, Validation, Writing – Original Draft Preparation, Writing – Review & Editing

Jairo Alexander Astudillo Lagos

INRAE, Toulouse, UMS 1337 TWB, France

Roles
Co-Author, Conceptualization, Software, Validation, Writing – Review & Editing

Anil Wipat

Newcastle University, Newcastle upon Tyne, England, UK

Roles
Co-Author, Conceptualization, Funding Acquisition, Project Administration, Supervision, Writing – Original Draft Preparation

Timothy J. Rudge

Newcastle University, Newcastle upon Tyne, England, UK

Roles
Co-Author, Project Administration, Software, Supervision, Writing – Original Draft Preparation

Katherine James

Newcastle University, Newcastle upon Tyne, England, UK

Roles
Co-Author, Conceptualization, Project Administration, Resources, Supervision
0000-0003-0167-8393

Jasper J. Koehorst

Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Gelderland, The Netherlands

UNLOCK, Wageningen, The Netherlands

Roles
Co-Author, Conceptualization, Data Curation, Formal Analysis, Funding Acquisition, Investigation, Methodology, Project Administration, Resources, Software, Supervision, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing
0000-0001-8172-8981

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