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OMERO Importer

General user discussion about using the OMERO platform to its fullest. Please ask new questions at https://forum.image.sc/tags/omero
Please note:
Historical discussions about OMERO. Please look for and ask new questions at https://forum.image.sc/tags/omero

There are workflow guides for various OMERO functions on our help site - http://help.openmicroscopy.org

You should find answers to any basic questions about using the clients there.

OMERO Importer

Postby calder » Wed Dec 08, 2010 5:46 pm

Hi folks,

I have started to test the Omero importer v4.2.2 with test images generated from some of my microscopes and I have run into a few of issues.

Files from Leica SP2 (.lei .tif) are imported fine except when I have XYZCT data. For some reason the Z is not read correctly (looks like it is only reading the first few z planes then repeating them to make up the correct z number for the stack). This problem also occurs running FIJI with latest BioFormats revision 7355 (7 Dec 2010 trunk). You can access the files (series 3: XTZCT image) from this link http://cmpdartsvr1.cmp.uea.ac.uk/downloads/bio-images/problem%20data/Leica%20SP2%20%2825-11-10%29/

Files from Zeiss 510 (.mdb .lsm) if you try and import .lsm files only when the .mdb file is present you get duplicated import (it appears to be importing all files associated with mdb for every lsm file you have selected. If you remove the mdb from the folder the lsm files import correctly. I have also checked files from Zeiss new ZEN software (lsm only) and import works fine. Note an option to switch on/off mdb import would solve this issue.

Files from Leica MZ16 stereo (LAS ver3.4) (xml .tif) image opens but meta data is incorrect. Same problem occurs when using FIJI. You can access the files from this link http://cmpdartsvr1.cmp.uea.ac.uk/downloads/bio-images/problem%20data/Leica%20MZ16%20stereo%20microscope%20%283-12-10%29/ additional info’http://cmpdartsvr1.cmp.uea.ac.uk/downloads/bio-images/problem%20data/Leica%20MZ16%20stereo%20microscope%20%283-12-10%29.txt

Files from a spinning disc confocal using MetaMorph software ver6.2r6 (.nd .stk .tif) has a bizarre problem. If I import using .nd file I get wrong the meta data but correct image. If I import using stk file then I get correct meta data but the wrong image. It appears to be caused by having another stk file with a similar name in the same folder i.e. image X. This also occurs when using FIJI bio formats importer. You can access the files from this link http://cmpdartsvr1.cmp.uea.ac.uk/downloads/bio-images/problem%20data/VisiTech%20QLC100%20spinning%20disc%20test%20images/ additional info’ http://cmpdartsvr1.cmp.uea.ac.uk/downloads/bio-images/problem%20data/VisiTech%20Spinning%20disc%20%2825-11-10%29.txt

OMERO is looking great and is going to make life a lot easier (appart from the usual bugs :lol: ). Just a thought that probably everyone esle has also said but it would look better and be easier for the end user if the importer and insight where one client.


Grant :D
Posts: 2
Joined: Mon Nov 29, 2010 5:16 pm

Re: OMERO Importer

Postby calder » Thu Dec 09, 2010 10:25 am

Just noticed that the z spacing for the Leica .lei file is wrong; looks like it is not converting z to microns but leaving it in metres.

G :)
Posts: 2
Joined: Mon Nov 29, 2010 5:16 pm

Re: OMERO Importer

Postby cxallan » Fri Dec 17, 2010 3:08 pm

Thanks for all of the feedback. I've inserted some tickets where we can track the resolution of some of these problems which are all gathered here:


We've been debating the best way to deal with the MDB / LSM issue for some time and we'll let you know when we come up with a good solution to the problem.
Site Admin
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