Standard metadata for 3D microscopy

Abstract

Recent advances in fluorescence microscopy techniques and tissue clearing, labeling, and staining provide unprecedented opportunities to investigate brain structure and function. These experiments’ images make it possible to catalog brain cell types and define their location, morphology, and connectivity in a native context, leading to a better understanding of normal development and disease etiology. Consistent annotation of metadata is needed to provide the context necessary to understand, reuse, and integrate these data. This report describes an effort to establish metadata standards for three-dimensional (3D) microscopy datasets for use by the Brain Research through Advancing Innovative Neurotechnologies® (BRAIN) Initiative and the neuroscience research community. These standards were built on existing efforts and developed with input from the brain microscopy community to promote adoption. The resulting 3D Microscopy Metadata Standards (3D-MMS) includes 91 fields organized into seven categories: Contributors, Funders, Publication, Instrument, Dataset, Specimen, and Image. Adoption of these metadata standards will ensure that investigators receive credit for their work, promote data reuse, facilitate downstream analysis of shared data, and encourage collaboration.

T-CLEARE: A Pilot Community-Driven Tissue-Clearing Protocol Repository

“…The goal of the WG was to establish standards to promote data sharing within the research community. The WG prioritized two approaches for developing standards: (1) to develop standard metadata, which has been described elsewhere (41); and (2) to investigate the feasibility of recommending standard protocols for tissue expansion microscopy. Because of the rapidly evolving nature of the field, the WG agreed that it was premature to recommend one or even a group of tissue-clearing protocols for use by all investigators.…”

The Brain Image Library: A Community-Contributed Microscopy Resource for Neuroscientists

“…BIL initially started with a simple metadata model that included ∼14 flexible fields for broad descriptions of the datasets. In 2021, BIL transitioned from this initial model to the 3D Microscopy Metadata Standards (3D-MMS) developed through a BRAIN Initiative standardization project 19 . The standard is in the process of being adopted by the International Neuroinformatics Coordinating Facility (INCF) 20 .…”

“…However, these resources are or were smaller in scale, limited in the size of the imagery they could accept, are based internationally, or may include images for many different fields and are not specifically tailored for neuroscience. developed through a BRAIN Initiative standardization project 19 . The standard is in the process of being adopted by the International Neuroinformatics Coordinating Facility (INCF) 20 .…”

The BRAIN Initiative Cell Census Network Data Ecosystem: A User’s Guide

“…While BIL does not limit the amount of data deposited per dataset or investigator, users planning to deposit more than 50TB of data in a single year should contact in advance to discuss data deposition plans. Data contributed to BIL following the Standard metadata for 3D microscopy schema (Ropelewski et al 2022) are issued DOIs. Higher-level traced neuron data is accepted in the SWC format (“NeuroMorpho.Org - a Centrally Curated Inventory of Digitally Reconstructed Neurons and Glia” n.d.).…”

“…Additional standards were adopted over the course of the project as they became available, e.g., the Essential Metadata for 3D Microscopy standard developed with support from the BRAIN Initiative (Ropelewski et al 2022) was recently implemented by BIL. The independent data generation within the BICCN allowed post-hoc assessment of standards for rigor and reproducibility via meta-analysis.…”