Open Microscopy Environment

Hi,

Someone has information on ATOM, a software to automated import images into OMERO. The project was initially developed by Olivier Mueller, but it stop in 2012
http://sourceforge.net/projects/auto-importer.

Or anybody have similar solution to automate transferts from microscope stations to OMERO server.

Philippe

Hi Philippe

Does OMERO.dropbox do what you want?

Simon

manics wrote:Hi Philippe

Does OMERO.dropbox do what you want?

Simon

Hi Simon,

OMERO-Dropbox could be very useful. However, I have some questions that I did find the answer in the documentation.
- What's happen to the files in the dropbox folders that have been synchronized ? Are the deleted to avoid duplication of data ?
- How to schedule or automate the image transferts to the server ? If users have to manually copy the files to the server where is the benefice compare to OMERO export client ?

Thanks

Philippe

Hi Philippe,

phm wrote:OMERO-Dropbox could be very useful. However, I have some questions that I did find the answer in the documentation.
- What's happen to the files in the dropbox folders that have been synchronized ? Are the deleted to avoid duplication of data ?

By default files that have been imported remain in the DropBox folders and so are duplicated. In this default configuration it is left to the user to manage their won DropBox space. However, you can configure DropBox to take advantage of the options available in In-place import such as,

Code: Select all

--transfer=ln_rm

to reduce duplication. This will, though, depend on your storage configuration.

There is also an, as yet, undocumented option,

Code: Select all

--transfer=upload_rm

which uploads the image files in the manner of a normal import and then deletes the original source files only upon completion of a successful import.

phm wrote:- How to schedule or automate the image transferts to the server ? If users have to manually copy the files to the server where is the benefice compare to OMERO export client ?

At present the only option would be for you to produce some sort of cronjob to transfer the acquired files into the DropBox directories. This still has some advantages over using manual import clients. However, we are planning to add more functionality to DropBox to address scheduled imports from remote storage.

Cheers,

Colin