Welcome to the OMERO metadata annotation and image import tool set!

This page hosts the documentation for:

1. OMERO Importer Python tool

2. REMBI-compatible metadata annotation Excel spreadsheets

3. OMERO Importer Excel Helper Python tool

The OMERO Importer Python tool was built by Alex Rigano in the Strambio-De-Castillia laboratory UMass Chan Medical School. It automatically adds metadata annotations to bioimage data and imports Images and metadata to OMERO.

The OMERO Importer reads metadata that has been entered into a Metadata annotation Excel spreadsheet with the help of the OMERO Importer Excel Helper and is used to annotate images it imports into OMERO.

If you want to use these tools, check out the Installation section.

Note

This project is under active development.

Contents

• Introduction
  • Research Data Management best practices
  • OMERO image data organization
• OMERO Importer
  • Use Case 1: No subdirectories in the Dataset folder
    • During the execution of an experiment
    • In preparation for Image data OMERO import
    • When you are ready to import your first images to OMERO
  • Use Case 2: Presence of subdirectories in the Dataset folder
    • During the execution of an experiment
    • In preparation for Image data OMERO import
    • When you are ready to import your first images to OMERO
• Metadata annotation Excel spreadsheet
  • Project TAB
  • Dataset TAB
  • Image-List TAB
• OMERO Importer Excel Helper
• Installation