Zebrafish HCS Import with OMERO¶

Scope¶

Target group¶

Scientists, scientific assistants, technical employees

Aim¶

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

Prerequisites¶

Install OMERO.insight on your local machine
(Optional) Install miniforge and omero-py

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, KNIME

Addressed step in the data life cycle: storage, management

Procedure¶

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

flowchart TD
    A[["Trigger
    End of Image Acquisition"]]:::trigger --> id1
    A[["Trigger
    End of Image Acquisition"]]:::trigger --> id2

    subgraph id1 [Image Import]
    B[1.Register your data in INTOB] --> C
    C[2.Import using OMERO.insight] --> D
    D[3.Metadata Enrichement]
    E[4.Attach Region of Interest - ROI] --> F
    F[5.Convert Data into a Plate]

    end

    subgraph id2 [Workflow Import]
    G[KNIME Workflow]
    H[Galaxy Workflow]
    end


    id1 --> I
    id2 --> I
    I[["Aim
    Image Data Sharing and management"]]:::goal

    click B href "#1-register-your-data-in-intob-and-elabftw"
    click C href "#2-data-upload"
    click D href "#3-metadata-enrichment-tags-and-kv-pairs"
    click E href "#4-associate-region-of-interest-roi-from-fish-inspector"
    click F href "#5-convert-your-data-into-a-plate"


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

Tasks¶

Register Data in INTOB and eLabFTW
Data upload
Metadata Enrichment: Tags and K/V Pairs
Associate Region of Interest: (ROI) from Fish Inspector
Convert your data into a plate

1. Register your data in INTOB and eLabFTW¶

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. For an overview:
Data Organization

2. Data upload¶

Data upload

3. Metadata Enrichment: Tags and K/V Pairs¶

Metadata Enrichment: Tags and K/V Pairs

4. Associate Region Of Interest (ROI) from FishInspector¶

Using Jupyter Notebook¶

If you do not have python on your personal computer, log-in into BIOTOX96/98
Open the terminal by typing "cmd" in the search bar
Type "activate omero_rdm"
Type "jupyter notebook". A browser windows will open
Browse in the Desktop and open the folder "OMERO RDM"
Open the Jupyter Notebook
Follow the instruction starting from "ROI Upload"

5. Convert your data into a plate¶

Login into OMERO.web
Click on the grinding weel on the top-right of OMERO.web
Select the script "UFZ/Dataset to Plate Well Name" and select the dataset to convert
Click "Execute Script"
Move the new plate into the scree

Workflow using KNIME¶

Image data, ROIs and metadata can be uploaded into OMERO using KNIME workflow.
KNIME workflow for the VAST/AIR data can retrieved at the WorkflowHub at this link.

Workflow using Galaxy¶

-- in preparation --