Open Microscopy Environment

Hi Melissa,

I have just imported some .lif files collected on a Leica DM6000. The images were captured with 2 channels, bright field and GFP, but upon importing to OMERO they are both being coloured blue and labelled '400'. I can change the colour manually by right clicking on the channel button but it is a bit of a pain to have to do this for every image. Do you think you could possibly have a look in to it and see if the bioformats could read the info better?

In addition (as I mentioned before regarding the other file types) the aquision date is the same as the import date (with a slight difference in time, 00:00 for aquision rather than the actual import time). These .lif files are very problematic for us as we cannot find the acquision date within the meta data at all (it must be there though?). Do you think you could also have a look at this for us? I can send you an image if you need one?

Many thanks,

Sam

Hi Sam,

I have just imported some .lif files collected on a Leica DM6000. The images were captured with 2 channels, bright field and GFP, but upon importing to OMERO they are both being coloured blue and labelled '400'. I can change the colour manually by right clicking on the channel button but it is a bit of a pain to have to do this for every image. Do you think you could possibly have a look in to it and see if the bioformats could read the info better?

I think this is the same problem reported here:

viewtopic.php?f=4&t=1198

which we've just now fixed as noted here:

http://trac.openmicroscopy.org.uk/ome/ticket/9243

In addition (as I mentioned before regarding the other file types) the aquision date is the same as the import date (with a slight difference in time, 00:00 for aquision rather than the actual import time). These .lif files are very problematic for us as we cannot find the acquision date within the meta data at all (it must be there though?). Do you think you could also have a look at this for us? I can send you an image if you need one?

I'm quite certain that this has also been fixed, so I would expect that upgrading to 4.4 once it is released will fix both problems. We can certainly double-check with one or two of your files, though, if you'd like. I will send you instructions for sending files in a private message.

Regards,
-Melissa