QUAREP-LiMi: a community endeavor to advance quality assessment and reproducibility in light microscopy

Abstract

The community-driven initiative Quality Assessment and Reproducibility for Instruments & Images in Light Microscopy (QUAREP-LiMi) wants to improve reproducibility for light microscopy image data through quality control (QC) management of instruments and images. It aims for a common set of QC guidelines for hardware calibration and image acquisition, management and analysis.quality of light microscopy imaging, please sign up at https://quarep.org/contact/.

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

“…In this spirit, the initial draft Microscopy Metadata specifications put forth by the 4DN ( 1, 2 ) IWG were evaluated and revised by the BINA QC-DM-WG ( 3 ), resulting in the current proposal. Furthermore, this process is being carried out in alliance with the QUAREP-LiMi initiative (( 9, 37 ) to ensure that all participating imaging community stakeholders (importantly including microscope and software tool manufacturers, who are ultimately responsible for providing the information to be recorded in microscopy metadata) are involved from the ground up and provide timely feedback. Because it is inherently impossible to predict all future changes the light microscopy field might undergo and in order to ensure rigor and reproducibility for image data now and in the future, it is essential that the 4DN-BINA (as well as future) extensions of the OME Data Model for bioimaging metadata proposed here are capable of gradually evolving to capture any future technical development while supporting FAIR data principles( 22, 28 ).…”

“…The specifications for the capture of metrics required for light microscope calibration and quality control captured in this extension were developed in collaboration with QUAREP-LiMi (quarep.org; Figure 5, and Supplemental Figures 1C and 4) (8,9,26,37,73) and are described in detail in an accompanying manuscript (21). A diverse set of metrics (41)(42)(43)(44)(45)(46)(47)(48)(49)(50)(51)(74)(75)(76)(77)(78)(79)(80)(81)(82)(83)(84)(85)(86) can be used to measure microscope performance and control image quality depending on the type of experiment being performed and the questions being asked.…”

“…Core model and Extensions - Metadata extension ( 26 ): An suite of extensions that expand the core of the OME Data Model ( 4, 5 ) to better capture state-of-the-art transmitted light and widefield fluorescence microscopy (Basic Extension), and confocal and advanced fluorescence modalities (Advanced and Confocal Extension). Importantly to improve the management of quality control, a novel data model for capturing instrument calibration procedures (Calibration and Performance Extension) was developed in close collaboration with QUAREP-LiMi ( 9, 37 ).…”

“…In order to foster widespread adoption of these 4DN-BINA-OME (NBO namespace) (26) specifications framework (Figure 1A, magenta bubble), parallel work is being conducted to develop userfriendly and when possible automated metadata collection tools (13,(27)(28)(29)(30); shared metadata storage best practices (Figure 1A, yellow bubble) (31)(32)(33)(34); as well as sustainable specifications to switch from proprietary formats for image data into common, cloud-ready OME Next-Generation File Formats (NGFF, Figure 1A, blue bubble) (35,36). Importantly, all of these activities are carried out in the context of the newly launched QUAlity Assessment and REProducibility for Instrument and Images in Light Microscopy (QUAREP-LiMi) initiative (quarep.org; (9,37) and involve several key members of the community, including microscope users, custodians, and manufacturers, imaging scientists, national and global bioimaging organizations, bio-image informaticians, standards organizations, and scientific publishers. The light Microscopy Metadata guidelines proposed here articulate along three orthogonal axes (Figure 1B):…”

Multidisciplinarity Is Critical to Unlock the Full Potential of Modern Light Microscopy

“…In recent years, open science projects, such as the development of open-source soft-and hardware, gained more and more traction among developers and users of light microscopy. Today, biologists have access to open-source software for image analysis and even microscope control (Carpenter et al, 2006;Edelstein et al, 2010;Schindelin et al, 2012). Open hardware projects (West, 2013;Mickoleit et al, 2014).…”