General Import Strategy with OMERO¶

Scope¶

Target group¶

Scientists, scientific assistants, technical employees

Aim¶

Enable UFZ users to upload and annotate their data in the OMERO UFZ instance.

Prerequisites¶

Install OMERO.insight on your local machine
(Optional) Install miniforge, omero-py or ezomero

Trigger event¶

The user wants to upload their image data in the OMERO UFZ instance for data management and sharing.

Categories¶

Applicable data types: Up to 140 different image file formats

Involved systems: OMERO UFZ instance

Addressed step in the data life cycle: storage, management

OMERO - General Import Strategy¶

We highlight in red colour the easier path for beginners


%%{ init: { 'flowchart': { 'curve': 'linear'}} }%%

flowchart TD
    A[["Trigger
    Image Acquisition"]]:::trigger --> id1

    subgraph id1 [Image Data Upload]
    B[OMERO.insight]:::red --> E
    C[CLI omero-py] --> E
    D[Galaxy] --> E
    F[Jupyter Notebooks] --> E
    E[Metadata  - OMERO.web]:::red
    end
    id1 --> G
    G[["Aim
    Sharing and Management"]]:::goal

    click B href "#data-upload"
    click C href "#data-upload"
    click D href "#data-upload"
    click F href "#data-upload"
    click E href "#omero-metadata"

    classDef trigger stroke:#00589c
    classDef goal stroke:#00589c
    classDef red fill:#FF474D