Nikon ND2: multi-location becomes series in wrong order
Posted: Fri Mar 27, 2015 6:25 pm
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
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