Importing many screening images

[wmoore]

We received this message on our QA feedback site, but it's easier to continue to conversation here (response to follow)

I have experienced few problems with OMERO that I would like to share and maybe get help.
- impossible to upload lots of file at once : I tried to upload a serie of 30 000 images from an acquisition done on a plate (it's a screen project) and it takes ages. It is actually impossible to tell if the system freezes or do something so I add to stop after a while.
- impossible to delete too much files at once : I tried to delete either a lot of images at once or several screens projects at once and it fails, after a long time nothing happens. Even trying to delete the general project containing several screens project fails.
- related to the import of several images : if there is a way to import lots of images at once, is there then a tool to organise images in a plate format as the direct import in a screen project would have done ? The idea is that sometimes you have a lot of images from a screen but they are regular tiff files and therefore cannot be recognised as coming from a screen (or is there an option upon importing those images ?)
- I recently imported images in the DIB format (acquired on the Cellomics instrument from Thermo), it's nice because when imported in the screen section the images are automatically imported in a plate format except that all images are shifted one column to the right, any idea why ?
thanks,
Julien

[wmoore]

Hi,

It seems a lot of your issues are discussed on this forum thread: http://www.openmicroscopy.org/community ... 34&p=10410

Presumably you're currently trying to import using the Insight client? For larger numbers of images this will certainly become less suitable, and you might want to look at importing via the command line http://www.openmicroscopy.org/site/supp ... mport.html or "OMERO dropbox" which monitors a directory on the server and imports any files dumped there: http://help.openmicroscopy.org/dropbox.html

You'll also find quite a bit of discussion of these by searching on our forums and you can read about more import options at https://www.openmicroscopy.org/site/sup ... arios.html

Deleting is quite a complex issue in OMERO (see https://www.openmicroscopy.org/site/sup ... elete.html)
One discussion of this is http://www.openmicroscopy.org/community ... 812&p=7189. As suggested, you might want to send us a log file from the server during failed deletes.

You can re-organise a Dataset of independent images into a Plate format using the "Dataset To Plate" script as described http://help.openmicroscopy.org/utility-scripts.html
This places each image in a new Well of a Plate.

Perhaps you could send us a screenshot of your DIB import in OMERO to illustrate the problem. Are the rows & columns named in the same way as in the Cellomics software? If there's a bug to be fixed here, it would really help to have a screenshot of the Cellomics software and and a sample of the data itself which you can upload to http://qa.openmicroscopy.org.uk/qa/upload/.

Hope that helps!

Will.