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Implementing a digital infrastructure for the lab using a central laboratory server and the SiLA2 communication standard.

ABSTRACT: In this report, a fully integrated solution for laboratory digitization is presented. The approach presents a flexible and complete integration method for the digitally assisted workflow. The worker in the laboratory performs procedures in direct interaction with the digitized infrastructure that guides through the process and aids while performing tasks. The digital transformation of the laboratory starts with standardized integration of both new and "smart" lab devices, as well as legacy devices through a hardware gateway module. The open source Standardization in Lab Automation 2 standard is used for device communication. A central lab server channels all device communication and keeps a database record of every measurement, task and result generated or used in the lab. It acts as a central entry point for process management. This backbone enables a process control system to guide the worker through the lab process and provide additional assistance, like results of automated calculations or safety information. The description of the infrastructure and architecture is followed by a practical example on how to implement a digitized workflow. This approach is highly useful for - but not limited to - the biotechnological laboratory and has the potential to increase productivity in both industry and research for example by enabling automated documentation.

SUBMITTER: Porr M

PROVIDER: S-EPMC7923558 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature

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Implementing a digital infrastructure for the lab using a central laboratory server and the SiLA2 communication standard.

Porr Marc M Lange Ferdinand F Marquard Daniel D Niemeyer Laura L Lindner Patrick P Scheper Thomas T Beutel Sascha S

Engineering in life sciences 20201209 3-4

In this report, a fully integrated solution for laboratory digitization is presented. The approach presents a flexible and complete integration method for the digitally assisted workflow. The worker in the laboratory performs procedures in direct interaction with the digitized infrastructure that guides through the process and aids while performing tasks. The digital transformation of the laboratory starts with standardized integration of both new and "smart" lab devices, as well as legacy devic ...[more]

PMID: 33716619

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Project description:Background:Digital Imaging and Communications in Medicine (DICOM®) is the standard for the representation, storage, and communication of medical images and related information. A DICOM file format and communication protocol for pathology have been defined; however, adoption by vendors and in the field is pending. Here, we implemented the essential aspects of the standard and assessed its capabilities and limitations in a multisite, multivendor healthcare network. Methods:We selected relevant DICOM attributes, developed a program that extracts pixel data and pixel-related metadata, integrated patient and specimen-related metadata, populated and encoded DICOM attributes, and stored DICOM files. We generated the files using image data from four vendor-specific image file formats and clinical metadata from two departments with different laboratory information systems. We validated the generated DICOM files using recognized DICOM validation tools and measured encoding, storage, and access efficiency for three image compression methods. Finally, we evaluated storing, querying, and retrieving data over the web using existing DICOM archive software. Results:Whole slide image data can be encoded together with relevant patient and specimen-related metadata as DICOM objects. These objects can be accessed efficiently from files or through RESTful web services using existing software implementations. Performance measurements show that the choice of image compression method has a major impact on data access efficiency. For lossy compression, JPEG achieves the fastest compression/decompression rates. For lossless compression, JPEG-LS significantly outperforms JPEG 2000 with respect to data encoding and decoding speed. Conclusion:Implementation of DICOM allows efficient access to image data as well as associated metadata. By leveraging a wealth of existing infrastructure solutions, the use of DICOM facilitates enterprise integration and data exchange for digital pathology.

Dataset Information

Implementing a digital infrastructure for the lab using a central laboratory server and the SiLA2 communication standard.

Publications

Implementing a digital infrastructure for the lab using a central laboratory server and the SiLA2 communication standard.

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