Open Microscopy Environment

Hi,

I have a question regarding Omero: I just updated one of my Omero folders (many of the files were already previously added to an Omero file), and Omero just made duplicates of all of these, which I then had to delete... My question is: is there a way to import a folder of data into Omero and for Omero to 'skip' or 'replace' the files that are already in there?? That would be very handy for folders that have large amounts of data, where it is not always obvious which are new files, and which are already on Omero.

Do yo have any feedback?

Thanks, and regards,
Jason

OMERO version 4.4.8

Hi Jason

Currently we do not offer such functionality i.e. we do not check if the files were already successfully imported.
Checking if the files are already imported will slow down the import process.
What are the use cases you were thinking about?
* import in the same dataset for example?
* replace the file if the file is already imported but somehow invalid?

Thanks

Jmarie

Hi Jmarie,
All of my confocal data is arranged in our Windows machine in folders (each folder is for a particular project, or a part of a project). Some of these folders have quite a large amount of confocal data in them (more than 100 files). When I import files into Omero from these folders, it is not at all obvious which files are already on Omero, and which ones need to be imported. Essentially I'm just looking for the easiest way to import my data into Omero without 1.) creating lots of duplicate files or 2.) spending lots of time checking files one by one to see if they've already been imported or not...
It would be ideal if I could just import the entire folder, and then have Omero only import the ones not already present (similar to how a Windows folder would behave - the 'skip' or 'replace' options.
Otherwise, is there perhaps a way to arrange files in Omero and the importer by date (or date of import in Omero)? That way all the new files would be at the top (or bottom) of the list, and I could more easily see which files need importing?

Thanks a lot,
Jason

Thanks for the feedback
It makes sense. We will be introducing the concept of Importset in OMERO 5 which will allow to easier identify files that have been imported and when.
The "checksum" checks that is already in place in OMERO5 could also allow identifying the files already imported so we could avoid duplicate import.

We will discuss the topic at one of our next client meeting, If you wish to be updated of prototype when ready, let me know.

Thanks

Jmarie

On the left panel of Insight there is an "Images" section that lists images by import date.