REMBI: Recommended Metadata for Biological Images—enabling reuse of microscopy data in biology

Abstract

Bioimaging data have significant potential for reuse, but unlocking this potential requires systematic archiving of data and metadata in public databases. We propose draft metadata guidelines to begin addressing the needs of diverse communities within light and electron microscopy. We hope this publication and the proposed Recommended Metadata for Biological Images (REMBI) will stimulate discussions about their implementation and future extension.

Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model

“…files). 2) The EMBL-EBI development of the REMBI recommendations for metadata to be included with imaging datasets deposited to BioImage Archive ( 60, 66, 97 ). 3) The development of the International Standards Organization (ISO) 23494-1 standard that will include the 4D N - B INA- O ME (NBO) Microscopy Metadata specifications as part of a Provenance information model for biological material and data ( 34, 98 ).…”

“…Furthermore, the increasing availability of public image repositories (e.g., Movincell ( 58 ), Image Data Resource - IDR ( 55 ), Electron Microscopy Public Image Archive - EMPIAR ( 59 ), Bioimage Archive ( 60 ), Allen Cell Explorer ( 61 ), the Cochin Image Database ( 62 ), the Cell Image Library ( 63 ), the RIKEN Systems Science of Biological Dynamics database - SSBD ( 64 ), and the NIH CELL Image Library ( 65 )), will undoubtedly increase the need for community-wide documentation and quality control standards, which can adapt to new technologies. As a first step in this direction ( 20 ) the Recommended Metadata for Biological Images (REMBI) ( 66 ) guidelines were recently proposed that would maximize the possibility of making bioimaging datasets available to other researchers in a timely manner, consistent with the FAIR principles (Findable, Accessible, Interoperable and Reusable) ( 22 ), and thus amenable for reuse.…”

QUAREP‐LiMi: A community‐driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy

“…GBI has published an overview of the current landscape for quality assurance and data management in imaging facilities, 14,15 including recommendations for QC. This document also highlights multiple aspects concerning image data standardization, management and publication, such as the definition of image and microscopy metadata guidelines and data models [7][8][9]14,[16][17][18] and the need to provide open access to all raw data for accepted manuscripts (e.g. Image Data Resource and BioImage Archive), [19][20][21][22] which are being addressed both within QUAREP-LiMi (see Working Group 7-Metadata) and by others [7][8][9]14,15,23 within the imaging community.…”

The European Bioinformatics Institute (EMBL-EBI) in 2021

“…REMBI, Recommended Metadata for Biological Images ( 27 ), was developed together with collaborators from over 30 institutions worldwide with the aim to maximise the potential for reuse of bioimaging data. In order for bioimaging data to fulfil their potential, it is essential for them to be systematically archived in public databases and to be accompanied by standardised metadata.…”