The OMERO Importer Python tool was developed at UMass Chan Medical School and in collaboration with the Canada BioImaging Open Science Project for use with the Canada BioImaging National OMERO Image Data Resource.
The OMERO Importer Python tool automatically reads bioimage data and metadata from a workstation running image acquisition or an associated NFS drive and imports it to an available OMERO repository.
Automated metadata annotation is carried out as follows:
- Experimental and sample description metadata is imported from customized metadata-collection Excel spreadsheets and written in OMERO as key/value pairs, tags, and OMERO.tables. Metadata annotation can be associated with a Project, Dataset, or Image as appropriate.
- NBO-Q compliant Microscopy metadata is imported from existing Microscope-Hardware- and Microscope-Settings.JSON files produced using the Micro-Meta App and attached to the relevant Image in OMERO. The content of these JSON files can then be visualized using the Micro-Meta App OMERO-plugin.
The OMERO Importer Python tool can be used in conjunction with Metadata annotation Excel spreadsheets and with the OMERO Importer Excel Helper Python tool to facilitate harvesting Image file names and capturing sub-directory structures into tag annotations.
More information about how to use these tools can be found on ReadTheDocs.