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ModuleAttributeCommentsData entry methodRelevant existing standards and ontologies
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Study
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(contains 1 or more Study components)Study typeType of the overall study, which may include other imaging and/ or non-imaging datatext, ontologyEDAM-BIOIMAGING, FBbi, EFO, IDR
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Study descriptionStudy description, e.g., title of published papertextIDR
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General dataset infoAuthors, publications, licenses etcmisc.Dublin Core, DataCite Metadata, schema.org, IDR
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Study component
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(contains Image data and Analysed data)Imaging methodTechnique used to acquire image dataontologyEDAM-BIOIMAGING, FBbi, OME
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Study component descriptionDescription specific to this image dataset componenttextIDR
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Biosample
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IdentityInternal unique ID
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Biological entityWhat is being imagedtext and/or ontology entry (multiple possible)EFO
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OrganismSpecies (multiple possible)taxonomyNCBI Taxonomy
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Intrinsic variableIntrinsic (e.g. genetic) alteration if applicabletext and/or ontology entry (multiple possible)EFO
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Extrinsic variableExternal biosample treatment (e.g. reagent) if applicabletext and/or ontology entry (multiple possible) or associated fileEFO, IDR
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Experimental variablesWhat is intentionally varied (e.g. time) between multiple entries in this study componenttext and/or ontology entry (multiple possible)EFO
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Specimen
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(linked to Biosample)Experimental statusTest/ control
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Location within BiosamplePlate/dish coordinate or tissue locationtext or associated fileOME
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Preparation methodSample preparation protocoltext, file, ontology, or widget for specific method typesEDAM-BIOIMAGING, FBbi
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Signal/contrast mechanismHow is the signal generated by this sampletext, ontologyEDAM-BIOIMAGING, FBbi
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Channel - contentSpecific specimen staining (e.g. IEM, DAB)text
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Channel - biological entityWhat molecule is stainedtext, ontology entriesEFO
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Image acquisition
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(linked to Specimen)Instrument attributesDetails about instruments usedtext, file, ontology, or widget for specific instrument typesEDAM-BIOIMAGING, FBbi, OME, 4DN-BINA-OME
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Image acquisition parametersImage acquisition detailstext, file, ontology, or widget for specific acquisition method typesEDAM-BIOIMAGING, OME, 4DN-BINA-OME
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Image data
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(result of Image acquisition, or processing of Image data)TypePrimary image/processed image/segmentationpull-downEDAM-BIOIMAGING
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Format & compressionFile typeextract from data if possibleEDAM-BIOIMAGING, OME
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Dimension extentsVolume in pixels: x, y, z, tiltsextract from data if possibleOME
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Size descriptionPhysical size of image volume in x,y,z & units (pull-down), OR magnificationextract from data if possibleOME
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Pixel/voxel size descriptionPhysical size of pixels in x, y, z & units (pull-down)extract from data if possibleOME
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Channel informationHow are individual channels represented in the imageextract from data if possibleOME
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Image processing methodImage registration, other processing applied to this datasettext, file, ontology, or widget for specific method typesEDAM-BIOIMAGING, FBbi
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Contrast inversion to TEMY/N; N if stained features result in brighter (whiter) signal; Y if it looks like a TEM imagepull-down
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QC infoQC score for uploaded image quality if applicabletext or controlled vocabulary
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Image Correlation
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(linked to 1 or more Image data)Spatial and temporal alignmentMethod used to correlate images from different modalities (e.g. manual overlay, alignment algorithm etc)text, ontologyEDAM-BIOIMAGING
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Fiducials usedFeatures from correlated datasets used for colocalizationtext
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Transformation matrix/ other infoCorrelation transformationstext, or related project files (e.g. .hx Amira files)
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Related images and relationshipCorrelated dataset or imageslink
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Analysed data
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Analysis result typeNumerical analyses, segmention (non-image), categorical features/phenotypestext, ontologyEDAM-BIOIMAGING, OME
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Data used for analysisSpecific feature set used for analysis (e.g. volume measurements, locations of features)text or file(s)
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Analysis method and detailsAnalysis methodtext, file, ontology, or pointer to Methods sectionEDAM-BIOIMAGING
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Referenced existing standards and ontologies
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EDAM-BIOIMAGING - an extension to the EDAM ontology (edamontology.org) for bioimage analysis, bioimage informatics, and bioimaging - https://bioportal.bioontology.org/ontologies/EDAM-BIOIMAGING
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FBbi - Biological Imaging Methods Ontology - https://www.ebi.ac.uk/ols/ontologies/FBbi
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OME - Open Microscopy Environment model, a specification for storing data on biological imaging - https://docs.openmicroscopy.org/ome-model/5.6.3/index.html
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IDR - Image Data Resource, a public repository of image datasets, and the associated data submission guidelines - https://idr.openmicroscopy.org/about/submission.html
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EFO - Experimental Factor Ontology, provides a systematic description of experimental variables, combines parts of several biological ontologies - https://www.ebi.ac.uk/efo/
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NCBI Taxonomy - curated nomenclature for all of the organisms in the public sequence databases - https://www.ncbi.nlm.nih.gov/taxonomy
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4DN-BINA-OME - minimum Information guidelines for fluorescence microscopy - https://github.com/WU-BIMAC/MicroscopyMetadata4DNGuidelines
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Dublin Core - a metadata element set for describing resources - https://dublincore.org/
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DataCite Metadata - core metadata properties for resource identification - https://schema.datacite.org/
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schema.org - schemas for structured data on the Internet - https://schema.org/
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Supplementary Figure 1. REMBI modules and attributes
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