Data can be linked from a fileserver to OMERO. This page explains how to do it and how to set it up for your institute fileserver.

Importing images from the CAi daten fileserver

Organizing your data in the dedicated folder

On the filesever \\cai.ad.hhu.de\daten, you must place your data in a dedicated folder that can be accessed by OMERO:

Z:\OMERO_in-place_import\AG_Xyz\Firstname_Lastname_HHUusername

Your group folders are created ahead and managed by the CAi. If you are not able to see them, let your admin know by email (tom.boissonnet@hhu.de) or via https://rocketchat.hhu.de 

You can arrange your folders then in whichever way you like. Note however that once imported, YOU SHOULD NOT RENAME any file or parent folder (this would break the link to OMERO).

We thus highly recommend you adopt a good organization from the start. Get in touch with us if you wish to discuss it ahead (ksenia.krooss@hhu.de , tom.boissonnet@hhu.de).

Two recommendation:

• Avoid nesting your folders too much. Data is organized in OMERO, and OMERO can tell you where the images are. Too many subfolders will just make it too hard to navigate
• Consistently name your folders. Start with the date YYYY-MM-DD, no space, not too long name, information from most generic to most specific:

2024-07-31_Arabidopsis_Mutation-XYZ_sample-1

Getting authorized to import data

The import is only made possible for those having access to the folders containing data. In your group folder in "OMERO_in-place_import\AG_Xyz", create the file "allowed_users.txt" (or edit it if it already exists) and add your username to the list (one HHU username per line).

Anyone in that list will be able to import the data located in subfolders.

Triggering the import from OMERO.web

Connect to https://omero-cai.hhu.de and open the script "import_script/Fileserver Import..."

"Data Type" and "IDs" are filled automatically from the selected container before starting the script.

• To generate Datasets inside a Project according to folder names, select the project in OMERO
• To attach all imported images to a single Dataset, select that dataset in OMERO
• For High-Content Screening data, select the screen to which you want to attach the generated plate

"Main folder path" is the root of what you will import. Subsequent subfolders may be used to name your datasets. From Windows File Explorer, select the full path by clicking right to the last folder name in the address bar:

File path will correspond to the relative path from the "main folder path" to the images you wish to import. For our above example, selecting the highlighted path as "main folder path":

• *.czi    will import all images with czi extension in the "main folder path"
• */image_3.czi      will import the image named "image_3.czi" in all subfolder from the "main folder path"
• *.czi, details/*.czi      will import all czi image in "main folder path" and all czi images in details folder. (multiple path are provided separated by a comma ",")

In the third scenario above, two Datasets will be created (if a Project was selected as Data Type). One named "2024-07-31_testfolder" with image_1.czi and image_2.czi, and a second named "2024-07-31_testfolder__details" with images from the details folder.