General Import Strategies¶

OMERO.insight and OMERO.web¶

OMERO stores image data on a central server. You can use the OMERO.insight client to upload, view and download data from any personal computer. The client could be downloaded from this link. UFZ OMERO server administrator will provide you with the server address to use when connecting from OMERO.insight. They may have set up a username and password for you too. Alternatively your username and password may be your standard login for the institution’s networked computers.

The Information Infrastructure for BioImage Data (I3D:bio) project facilitates the uptake of OMERO into research data management (RDM) practices at universities and research institutions in Germany. Since the adoption of OMERO into researchers' daily routines requires intensive training, a broad portfolio of training resources for OMERO is an asset. On top of using the OMERO guides curated by the Open Microscopy Environment Consortium (OME) team, imaging core facility staff at institutions where OMERO is used often prepare additional material tailored to be applicable for their own OMERO instances. Based on experience gathered in the [Research Data Management for Microscopy group (RDM4mic)] (https://gerbi-gmb.de/activities/rdm4mic/) in Germany, and in the use cases in the I3D:bio project, I3D:bio created a set of reusable, adjustable, openly available slide decks to serve as the basis for tailored training lectures, video tutorials, and self-guided instruction manuals directed at beginners in using OMERO. The material is published as an open educational resource complementing the existing resources for OMERO contributed by the community.

Resources¶

Data Organization in OMERO¶

The following guidelines are given in order to have a consistent data and metadata structure in OMERO. For further and indeep information please refer to the I3D:bio's OMERO training material (202310_GENERAL_OMERO_Material_06-0_DataOrganization.pdf)

Managing data in classical file folder hierarchies¶

It is important to remember that:

OMERO is not intended for use as a file hierarchy system
OMERO is object-oriented

How to organize data in OMERO?

Structure data according to your (group‘s) needs
Make use of Tags (and/or Key-Value Pairs) for data organization (instead of deep folder hierarchies)
Explore ways of data organization and discuss them with your research group

RDM Tools to use in combination with OMERO¶

eLabFTW¶

eLabFTW is a free and open source electronic lab notebook. UFZ has a eLabFTW instance to record your experiments and keep track of your experimental design. We strongly recommend to use this tool to add information to your study design according to the REMBI guidelines.

An example of a REMBI annotated study for a HCS study can be found here.

INTOB¶

INTOB is an integrated software and database for effect observations on organism scale. In case you are performing a Fish Embryo Test (FET) experiment, please add it to this database in order to keep track of additional experimental metadata.

Useful Examples¶

Example of REMBI for Study Description
Example of K/V pairs for HCS zebrafish image data

ETOX - Data Workflows¶

Scope¶

Target group¶

Scientists, scientific assistants, technical employees

Aim¶

...

Prerequisites¶

Access to XYZ
Access to Data XYZ ...

Trigger event¶

...

Categories¶

Applicable data types: png, xls, csv, netcdf, ... (all types)

Involved systems: OMERO, eLabFTW, INTOB-DB

Addressed step in the data life cycle (see for help):

High content screening (HCS) assay with zebrafish embryos¶

Standards Operation Procedure (SOP) for HCS images, ROIs and K/P values upload¶

The present SOP is intended to be used for data produced with the VAST and AIR imaging systems in the ETOX department. Please read the session OMERO at UFZ before starting the workflow to have an overview on the different tools and metadata schema**

Before starting¶

Experiment needs to be recorded in the INTOB database. Before starting your HCS study, it is highly recommended add the study description in the eLabFTW. An example of a good REMBI study information description is give here
Prepare your data structure in OMERO.web (Create a Project folder or a Screen)

Procedure¶

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

flowchart TD
    A[["Trigger
    Finished data processing"]]:::trigger --> id1

    subgraph id1 [SOP OMERO]
    B[1. Image acquisition] --> C
    C[2. OMERO image upload] --> D
    D[3. OMERO ROI upload] --> E
    E[4. ...] --> F
    F[5. OMERO key/value pair upload]
    end
    id1 --> G
    G[["Your final goal"]]:::goal

    click B href "../../practice-ufz/DMP/acquire_upload_images/"
    click C href "../../practice-ufz/OMERO/acquire_upload_images/"
    click D href "../../practice-ufz/OMERO/upload_roi/"
    click E href "../../practice-ufz/DMP/convert_dataset_plate/"
    click F href "../../practice-ufz/DMP/upload_key_pair_values/"

    classDef trigger stroke:#00589c
    classDef goal stroke:#00589c

Tasks¶

In preparation