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WU-BIMAC / NBOMicroscopyMetadataSpecs

The 4DN + BINA Tiered System of Microscopy Metadata Guidelines was developed by the 4DN Imaging Standards Working Group in collaboration with the BINA Data Management and Quality Control Working Group (https://www.bioimagingna.org/qc-dm-wg) for documenting microscopy experiments and assessing the quality of image data.
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STRAMBIO-LACOSTE -- Add Imaging Mode to Channel? #82

Open strambc opened 2 years ago

strambc commented 2 years ago

Element name(s): Channel

Justification for the addition (brief and compelling): your input here

Full description of the proposed addition (enough detail to implement): your input here

Source of change (e.g., #XXX issue with change request):
Suggested by Judith Lacoste

Brief description of the change and its rationale (short and compelling):
your input here

New Element name: __

New Field name: Imaging Mode

New Element/Field description: __

New Element/Field Tier: Tier 1

New Field Data type: Enum

New Field requirement level: REQUIRED

New Field enumeration value(s): Use values from attached document

Technology-organisation-schema_Euro-BioImaging-2022.pdf

https://www.eurobioimaging.eu/upload/Technology-organisation-schema_Euro-BioImaging-2022.pdf

strambc commented 2 years ago

Currently, we have a field called:

Channel/IlluminationType with enumeration values drawn from

https://ontobee.org/ontology/FBbi?iri=http://purl.obolibrary.org/obo/FBbi_00000345

Should this be merged or different?

strambc commented 2 years ago

Also we have a field called:

Experiment/IlluminationMethod with enumeration values drawn from

http://purl.obolibrary.org/obo/FBbi_00000031

Should this be merged or different?

JSDLacoste commented 2 years ago

I feel they should be left separated despite the fact that they overlap significantly. It is a reality that the fluorescence labeling of the samples is not always a perfect match with what is available on a particular microscope. Keeping them separated will help microscopy reproducibility in the long term.

JSDLacoste commented 2 years ago

Secondly, when looking/browsing at microscopy datasets in OMERO, it's important to know if the images are laser scanning, tirf, spinning disk etc. The IDR.openmicroscopy.org suffers there. 65 datasets are marked as "Fluorescence microscopy", that could be epifluorescence, laser scanning, etc. Interpretation of the data could be different.