Open Microscopy Environment

Hi,
I just uploaded a file "Acq5x5in384well_well1001.nd2" to the QA system (ID: 10945) which consists of 25 images of micro-array spots acquired with a Nikon Elements-based system. Upon import with BioFormats 5.1-m4 it shows up OMERO as a series of individual images per:

Due to the naming of the series #'s, the order is messed up. Could it be made so the series numbering is made into: "(series 0000x)" i.e. use something like "%05d" formatting in the generation of that name?

Just to provide a bit of background: in our application these micro-array spots are effectively the same as very high density multi-well experiments (think of it as 40 by 120 mini-wells on the footprint of a slide) so once the are imported as series in OMERO I will run the Dataset_To_Plate script to convert it into a Plate layout.

Btw. this new behavior in 5.1-m4 where BioFormats makes those multi-location ND2's into series is already much better than the earlier behavior that generated Z-stacks. Thanks!!!

Thanks,
- Damir

Hi Damir,

thanks for uploading the sample file.
I created a ticket for this issue: https://trac.openmicroscopy.org/ome/ticket/12809

Kind Regards,
Dominik

Hi Dominik,

Thanks for getting this into the "queue". One small clarification: we typically generate images sets where there are well over 1000 images in a "series" so would be good if enough pre-pended 0's are generated to keep the order accurate. These images are of high-density spotted (=printed) cell-spot microarrays on either a slide or a chamber in a 4-well plate where in the imaging step we visit each cell-spot to create a multi-channel image of that spot. Each cell-spot is different so keeping the images correctly ordered is critical for us.

Thanks,
- Damir

Hi Damir,

following up on this thread, a Pull Request has been opened, reviewed and merged into the development line to sort this issue.

The series naming improvements for Nikon ND2 files should be included as part of the OMERO/Bio-Formats 5.1.1 release due by the end of this month.

Best regards,
Sebastien

Thanks Sebastien, much appreciated by me and hopefully of value to others as well.
Damir