QUAREP-LiMi. Development of quality control tools and methodologies for light microscopy: improving image data quality, reliability & reproducibility.

Background: since their introduction and widespread use in the late 17th Century, microscopes have moved from qualitative, image-collecting tools to automated, complex instruments capable of acquiring information-rich images. Indeed, microscopy now underpins a lot of biomedical research and is being used to provide the spatial context to many emerging 'omics' techniques. Observing a sample is often insufficient; there is a need to back-up these observations with quantitative information to answer often complex biomedical questions. The quality of these observations and data are only as good as the quality of the microscope used to make them: thus, it is important that microscope 'quality' is understood, documented and made available. With this information to hand, researchers and the public will have full confidence in the imaging data collected, interpreted and published from such instruments.
The problem: standardisation for fluorescence microscopy is not widely practised in the scientific community: a recent large (from approximately 200 imaging labs) global microscopy-user community survey performed by members of the Co-I team have highlighted the inconsistencies when it comes to choosing which microscope Quality Control (QC) metrics to record and how frequently they are performed.
The solution: we have established an international consortium of microscopists and other related users/ groups, QUAREP-LiMi (QUality Assessment and REProducibility for Instruments & Images in Light Microscopy) with an initial aim to gain consensus across the microscopy community and identify a set of QC tests that should be performed on microscopes at defined intervals. This will, we hope, 'demystify' the subject and encourage good practise for microscope maintenance and promote standardisation between labs and research facilities employing light microscopy. Working with microscope and microscope component manufacturers, we will seek to automate the process of QC data capture and analysis with an intent to store this 'microscope quality' information in the image metadata (information about an image that describes how that image was captured). We will ensure that all developed protocols, samples and image analysis tools are made freely available and accessible to both experienced and inexperienced microscopists. The work of QUAREP-LiMi will raise the profile of, and the need for, better quality control within light microscopy and as a result, we hope will influence policy makers and ensure that a minimal set of metadata that describes microscope 'quality' are made available with all published microscopy images. For this, we are working with publishers, image data repositories and funding bodies.
The need for funding: QUAREP-LiMi has grown rapidly to over 270 members from both academic and commercial backgrounds and consists entirely of voluntary members. Organising and managing such a large and disparate group is difficult and time consuming, with this funding bid, we will employ a technical project manager to manage, coordinate and effectively communicate the work of the consortium.
Impact: if the aims of QUAREP-LiMi are realised, a number of communities and stakeholders will benefit:
1. Research scientists and imaging scientists will take advantage of the harmonization and simplification of the QC procedures.
2. Scientific publishers and the general public will profit from an overall enhanced trust in the value and reproducibility of scientific publications.
3. Funding bodies will benefit from the planned improvement of QC practices that will undoubtedly improve image data reliability, reproducibility, and openness, increasing overall the value and quality of scientific output.
4. Core imaging facilities and microscope custodians and users, who will profit from heightened confidence in the accuracy of their image data and the suitability of performed QC measurements to answer their scientific questions.

Standardisation for fluorescence microscopy is poorly practised in the scientific community: a recent UK survey and an ELMI survey we conducted highlighted the inconsistencies when it comes to choosing which microscope Quality Control (QC) procedures to perform and how frequently they are carried out. Understanding microscope performance is essential when deriving quantitative data from captured images, but there are no standards for reporting such QC information. We have established an international consortium: QUality Assessment and REProducibility for Instruments & Images in Light Microscopy, QUAREP-LiMi, made up of microscopists, manufacturers, funding bodies, publishers and standard-setting organisations. The aim is to develop a set of microscope QC samples, tests and define quality assessment procedures that should be performed on light microscopes at regular intervals. These we will target, promote and make applicable to both inexperienced and experienced microscopists with the intention of gaining widespread adoption by anyone using a microscope. We have split QUAREP-LiMi into individual working groups each focussing on an identified aspect of microscope or micrograph QC.
Working with publishers, QUAREP-LiMi aims to influence policy, to ensure that at the point of publishing microscopy data, the 'quality' of that data is defined with respect to the instrument used to make those observations.
QUAREP-LiMi has 277 members from across the globe, all of which are providing their time and effort voluntarily. Membership is split between academia (66%) and industry (26%) with participation from Standard-setting bodies, funders and publishers.
Organising and managing a large and disparate group is becoming difficult, and with this funding we will employ a technical administrative person to oversee, manage and effectively communicate the work of QUAREP-LiMi both internally and externally. This will enable us to expand, and more effectively support our objectives.