Cheat sheet: Light microscopy

Optical Light Microscopy

Description

Light microscopy technologies are widely adopted in modern biological and medical research projects. As the field grows, the number of imaging techniques, processing methods as well as the size of the data increases. To avoid loss or degradation of data in the late stage of a project period and after the end of the project, data management of light microscopy data needs to be considered, planned and executed throughout the data life-cycle.

Type of data/experiments/methods

OME-tiff

OME-tiff
Open Format
Currently preferred format

OME-NGFF

OME-NGFF
Open Format
Upcoming
Optimized for (cloud) object storage and partial transfer

HDF5

HDF5 Library and File format
Open Format

CZI-zeiss

Zeiss
Proprietary format

LIF

Leica
Propriertary format

ND2

Nikon
Propriertary format

PNG, JPEG, TIFF

Lossy formats
Not recommended for storing microscopy image

Metadata Standards

Recommended Metadata for Biological Images (REMBI)

REMBI article: Sarkans, U., Chiu, W., Collinson, L. et al. REMBI: Recommended Metadata for Biological Images—enabling reuse of microscopy data in biology. Nat Methods 18, 1418–1422 (2021)
REMBI reference

Ontologies

General:

Sources for Reusable Data

IDR

A public repository for reference imaging datasets. Research community can submit search and access the raw datasets and analyses.
Usually CC0 or CC BY 4.0
Identifiers:
- DOI and accession number for all datasets
- See also: Ontologies
- Other identifiers: Targets (genes/proteins): Gene IDs/UniProt Protein accession IDs
Access possible through API and direct download, you can run image analysis workflows directly on IDR datasets on usegalaxy.no using the IDR download tool

BioImageArchive

Free, publicly available online resource which stores and distributes biological images
Some accessions have individual licenses - these are explicitly stated on the page for that accession. Where no license is stated, data is available under the EMBL-EBI Terms of Use
Identifiers:
- BioImage Archive accession number
- DOI for selected datasets
- See also: Ontologies
- Other identifiers: Targets (genes/proteins): Gene IDs/UniProt Protein accession IDs
Access possible through webinterface, direct download and API

Storage and Computing

Nels
usegalaxy.no can be used to run image analysis workflows
UiO Storage Hotel

Data Deposition Repository

IDR

usually CC0 or CC BY 4.0
Identifiers:
- DOI and accession number for all datasets
- See also: Ontologies
How to submit to IDR
Scheduling a release date is possible with limitations

BioImageArchive

Specification of license possible - usually CC0 or CC BY 4.0. Where no license is stated, data is available under the EMBL-EBI Terms of Use
Identifiers:
- BioImage Archive accession number
- DOI for selected datasets
- ORCID for authors
- See also: Ontologies
- Other identifiers: Targets (genes/proteins): Gene IDs/UniProt Protein accession IDs
How to submit to BioImageArchive
Embargo until publication possible