Open Microscopy Environment

Hello,

we are currently transferring images from our omero database to a new omero database.

we have about 230 go to transfer.

on omero we annotate all images. And we spent a lot of time doing this description.

to avoid losing our annotations we want to export the images in batch and in the format ome.tiff to keep all the annotations.

we use the scipt export (Batch_Image_Export) with omero insight.

we have problems, to export large files (> 1go).

and when we select a lot of small images, export is not possible either.

to export large volumes in OME.Tiff there prerequisites in the system settings of our database?

is there another way to export our images by keeping the annotations?

thank you for your help

Regards,

sameh

Hi Sameh,

the ome.tiff export doesn't export the annotations, so that won't work.
Why do you want to export and reimport the images? Usually one would just
copy / upgrade the database. What version is the old and the new system?

We have some scripts for copying annotations over from one server to another,
which you could use as template. But it would be good to check first if that's
really the best approach for what you want to achieve.

Regards,
Dominik

Dear Sameh,

There is a lot that could be done for bulk transfer of data from one OMERO server to another; unfortunately, it is not trivial and is not yet slated for a coming release. In the meantime, could it work to simply create the new OMERO server from a backup of the existing one? If not, do you also need to preserve attached files?

You will have noticed that OME-TIFF export does in fact preserve some annotations. Though, for instance, you may find that at the other end you have duplicate tags and need to write a script to merge them. What kinds of annotations are the most important to preserve?

Cheers,
Mark

Dominik wrote:Hi Sameh,

the ome.tiff export doesn't export the annotations, so that won't work.
Why do you want to export and reimport the images? Usually one would just
copy / upgrade the database. What version is the old and the new system?

We have some scripts for copying annotations over from one server to another,
which you could use as template. But it would be good to check first if that's
really the best approach for what you want to achieve.

Regards,
Dominik

Hello Dominik,

indeed we need to transfer the annotated data from our omero server to another omero server. our new database is hosted at another infrastructure in France.

our database is in version 5.4.6 and the new database is in version 5.4.4


what is important for us is to keep the tags. because it takes a lot of time to redo everything.

we tried to export and import our images in ome.tif format, this format retains the tags.

but our problem is that we can not export big data. and we wonder if there are prerequisites in the system settings.


thank you for your ideas and your help

mtbc wrote:Dear Sameh,

There is a lot that could be done for bulk transfer of data from one OMERO server to another; unfortunately, it is not trivial and is not yet slated for a coming release. In the meantime, could it work to simply create the new OMERO server from a backup of the existing one? If not, do you also need to preserve attached files?

You will have noticed that OME-TIFF export does in fact preserve some annotations. Though, for instance, you may find that at the other end you have duplicate tags and need to write a script to merge them. What kinds of annotations are the most important to preserve?

Cheers,
Mark

Hello,

thank you for your reply ,

we need to keep the tags.

we tried with the format ome tif format and it works.

and after the import we use a scipt to merge the tags, and it works too.

the main problem is that we can not export big data in batch.

we wonder if there are prerequisites in the system settings.

Thank you for your help

You are right, tags are indeed exported, sorry about that. What do you mean with "big" images exactly? Are these large 5D images or pyramidal images?

Regards,
Dominik

Dominik wrote:You are right, tags are indeed exported, sorry about that. What do you mean with "big" images exactly? Are these large 5D images or pyramidal images?

Regards,
Dominik

yes it is 5D images,

when I select several 5D images to export in batch, the zip file is not created

Dear Sameh,

It's still sounding as if your easiest option at this time would be to simply create the new OMERO server from a backup of the existing one. It would work fine to restore a 5.4.6 binary repository and database to run under a 5.4.4 server.

In case that's not an option: The tags you need to preserve, what are they on? Do the most valuable ones just tag the images, or are you tagging other objects like ROIs? (OMERO makes a lot possible, even beyond what the graphical clients offer.) It could make sense to write a script that connects to both servers at once to copy the tags from a group on one to a group on the other based on matching image names or whatever.

Cheers,
Mark

Dear Sameh,

Also, what are the typical dimensions of your 5D images? (X, Y, Z, C, T)

Cheers,
Mark

mtbc wrote:Dear Sameh,

Also, what are the typical dimensions of your 5D images? (X, Y, Z, C, T)

Cheers,
Mark

hello

we have different images,

for example;
- 1024x1024 32Z 1C 20t
- 3216x3216 1Z 3C 1t