Table 2 Tiers for light microscopy metadata reporting as proposed by the IWG of the 4DN initiative and by the QC-DM-WG of BINA

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

Category

Nr.

Name

Description

Examples

Descriptive

1

Minimum Information/ Qualitative or Basic Quantification/ Material & Methods

Developmental and stem-cell biology experiments in which qualitative analysis of image data is used to support major findings, transfection control, viability assay, counting of cells and nuclei, expression level measurements and localization of markers in cellular subcompartments

Histochemistry, immunohistochemistry, fluorescence in situ hybridization (FISH), immunofluorescence, fluorescent protein labeling

Analytical

2

Advanced Quantification

Reporting quantitative effects that require advanced quantification, including the localization of single molecules and tracking of intracellular dynamics

Diffraction-limited spot localization, measurement of distances, colocalization studies, detection of low-signal features, advanced processing, cell tracking and single-particle tracking, dynamic expression level quantification

3

Manufacturing/ Technical Development/ Full Documentation

Full documentation of microscopic setup, image acquisition and quality control

Microscopy hardware manufacturing, development of novel and yet-to-be-validated technology in both commercial and academic settings, full reproducibility of microscopy setup and image acquisition settings

  1. Each tier accommodates increasingly complex images, experiments, instrumentation and analytical needs and therefore requires progressively more metadata. This tiered system is not intended to meet the needs of all imaging communities; rather, it is proposed as a framework that might need to be adapted and modified depending on the needs of individual data collection consortia, disciplines or institutions.
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