A global view of standards for open image data formats and repositories

Abstract

Imaging technologies are used throughout the life and biomedical sciences to understand mechanisms in biology and diagnosis and therapy in animal and human medicine. We present criteria for globally applicable guidelines for open image data tools and resources for the rapidly developing fields of biological and biomedical imaging.

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

“…13 BioImaging North America (BINA, https://www.bioimagingna.org/) and the RT-MFM technological network (Microscopie photonique de Fluorescence Multidimensionnelle, http://rtmfm.cnrs.fr/). 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.…”

“…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.…”

“…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 Euro-Bioimaging ERIC includes the independent assessment of QC measures and implementation in the ongoing evaluation of existing Nodes and during the application process for new imaging Node candidates.…”

“…WG7 aims to systematically evaluate the structure and semantics of the initial 4DN-BINA-OME (NBO) extension proposal [7][8][9] and to launch a coordinated outreach and training strategy towards reaching a community-wide consensus around the proposed metadata specifications and the adoption of these specifications by public image data repositories. 14…”

A Systematic, Open-Science Framework for Quantification of Cell-Types in Mouse Brain Sections Using Fluorescence Microscopy

“…To begin using our image processing and analysis workflow the user first runs a file management script (step 1 7 ) and loads their image files into FIJI-ImageJ. This script takes image series stored in a proprietary file format (e.g., ".lif, " ".czi, " and ".oir, " for Leica Microsystems, Zeis Microscopy, and Olympus Microscopy, respectively) and exports these image series in 7 https://github.com/SwayneLab/PFIA/blob/main/pfia_step_1_file_mgmt.ijm a ".tif " (a file format that complies to FAIR specifications, (Wilkinson et al, 2016;Swedlow et al, 2021). Files are organized into an "output" folder, comprising subdirectories for each image series and subsequent associated files.…”