OMERO Import

A common workflow that we recommend to use to import images into OMERO. Instead of duplicating images and using more storage space, we recommend users to use in_place import

• Import data by moving images to Nemo.

  

• OMERO import the images and owns the images.

Step-by-Step

1. Connect to Nemo

   • connect to server(Mac)

     • smb://data2.thecrick.org/proj-omero/<id>

   • map network (Ms Windows)

     • \\data2.thecrick.org\proj-omero\<id>

2. Create a folder/directory in proj-omero/<id>

3. Copy your images to that folder

4. Current procedure is to contact Ken Ho and let him know the folder to be imported.

• A snapshot of your images will be automatically backup by Nemo every night, import to OMERO will occur after that.

• We hope to automate this process in the near future.

Shallow folder structure

• We prefer shallow folder structure as OMERO can only accept 2 level of organisation, project and dataset.

Filename

We recommend you to use

• Portable Operating System Interface (POSIX) file name (IEEE 1003, ISO/IEC 9945)

  • https://www.ibm.com/docs/en/zos/2.2.0?topic=locales-posix-portable-file-name-character-set

  • https://en.wikipedia.org/wiki/POSIX

  • To simplify conversion requirements, use the POSIX portable file name character set when naming your files:

    • Uppercase A to Z

    • Lowercase a to z

    • Numbers 0 to 9

    • Period (.)

    • Underscore (_)

    • Hyphen (-)

  • Avoid these characters: @ $ % & / : * ? ” ‘ < > | ~ ` # ^ + = { } [ ] ; !” , white space (no space please), tab

  • ASCII supported characters only (problems of European or Asian characters compatibility among Windows/Mac/Linux OS filenames

• If you want to use dates in your filename, please use ISO 8601 format, i.e. 2023-11-03

  • (ref: https://en.wikipedia.org/wiki/ISO_8601)

• One suggestion: Date-PI_ID-organism-sample_type-fluorescent_probes-treatment-replicate

Network speed consideration

• Please transfer your images when you are using your computer attached with a wire ethernet cable CAT5 or above to do the transfer.

• We would strongly recommend you NOT to transfer your files using your laptop at home via VPN

• If your image set is large, i.e. > 200GB, please let us know the location on Nemo, we can ask HPC colleagues to transfer that for you.

• If you have a large dataset, i.e. > 1TB, please contact Ken (kenneth.ho@crick.ac.uk)

Storage and quota

• At present, the OMERO service is free. It is funded through Advanced Light Microscopy STP

• The proj-omero storage is used mainly for image data and not for binary program or other file types.

Ownership (in computing term)

• After OMERO imported your images, your images will be owned by the OMERO server. However, you will still have read access to the original file data.

  • In computing terms, the omero application runs under a special user ID called omero.

  • The application runs under user id omero owns (in computer terms) all the imported images.

  • Imported image data still belongs to you and your lab.

  • OMERO server is managing them on behalf of you and your lab.

  • If you or your lab explicitly wants to remove a specific set of image data from Nemo network storage, please contact us and we can do that for you.

• Image data managed by omero are all stored on Nemo network storage and are managed and backed up under usual Nemo operation, so it is the same as saving your images to Nemo directly.

Access/(not download)

Access/(not download)