names of channels with lif format
Posted:
Tue Mar 19, 2019 8:58 amby sameh
Hello Omero team,
I noticed a problem when I import images in Lif format.
the order of the channels and the luts are correct but the names of the channels are not correct.
for example, for some images there is the same name for two different channels.
is this related to the bioformat library?
thank you for your help
Sameh
Re: names of channels with lif format
Posted:
Tue Mar 19, 2019 2:52 pmby dgault
Hi Sameh,
This sounds like it is probably an issue with Bio-Formats parsing the channel names. Would you be able to upload a sample file displaying this problem to
https://www.openmicroscopy.org/qa2/qa/upload/?
David Gault
Re: names of channels with lif format
Posted:
Tue Mar 19, 2019 3:24 pmby sameh
dgault wrote:Hi Sameh,
This sounds like it is probably an issue with Bio-Formats parsing the channel names. Would you be able to upload a sample file displaying this problem to
https://www.openmicroscopy.org/qa2/qa/upload/?
David Gault
ok, I uploaded 3 samples files displaying this problem.
thank you
Sameh
Re: names of channels with lif format
Posted:
Wed Mar 20, 2019 4:25 pmby dgault
Thank you for uploading the files. I can certainly reproduce the issue and it does indeed look like a Bio-Formats bug. Can you confirm if the below channel values would be correct for each file:
sameh.lif
Bio-Formats currently reports:
Channel 1: Leica/ALEXA 488
Channel 2: Leica/ALEXA 568
Channel 3: Leica/ALEXA 488
From parsing the file I can read:
Channel 1: Leica/ALEXA 488
Channel 2: Leica/ALEXA 568
Channel 3: Leica/ALEXA 647
sameh1.lif
Bio-Formats currently reports:
Channel 1: Leica/ALEXA 594
Channel 2: Leica/ALEXA 488
From parsing the file I can read:
Channel 1: Leica/ALEXA 594
Channel 2: Leica/ALEXA 488
sameh2.lif
Bio-Formats currently reports:
Channel 1: Leica/HOECHST 33258
Channel 2: Leica/ALEXA 488
Channel 3: Leica/ALEXA 594
Channel 4: Leica/ALEXA 647
From parsing the file I can read:
Channel 1: Leica/DAPI
Channel 2: Leica/ALEXA 488
Channel 3: Leica/ALEXA 594
Channel 4: Leica/ALEXA 647
Re: names of channels with lif format
Posted:
Thu Mar 21, 2019 9:53 amby sameh
dgault wrote:Thank you for uploading the files. I can certainly reproduce the issue and it does indeed look like a Bio-Formats bug. Can you confirm if the below channel values would be correct for each file:
sameh.lif
Bio-Formats currently reports:
Channel 1: Leica/ALEXA 488
Channel 2: Leica/ALEXA 568
Channel 3: Leica/ALEXA 488
From parsing the file I can read:
Channel 1: Leica/ALEXA 488
Channel 2: Leica/ALEXA 568
Channel 3: Leica/ALEXA 647
sameh1.lif
Bio-Formats currently reports:
Channel 1: Leica/ALEXA 594
Channel 2: Leica/ALEXA 488
From parsing the file I can read:
Channel 1: Leica/ALEXA 594
Channel 2: Leica/ALEXA 488
sameh2.lif
Bio-Formats currently reports:
Channel 1: Leica/HOECHST 33258
Channel 2: Leica/ALEXA 488
Channel 3: Leica/ALEXA 594
Channel 4: Leica/ALEXA 647
From parsing the file I can read:
Channel 1: Leica/DAPI
Channel 2: Leica/ALEXA 488
Channel 3: Leica/ALEXA 594
Channel 4: Leica/ALEXA 647
Hello,
yes the channels values are correct !
Re: names of channels with lif format
Posted:
Fri Mar 22, 2019 2:51 pmby dgault
Thank you for confirming, I have created a Bio-Formats Trello card to track the issue:
https://trello.com/c/e9WH7Lvd/363-incor ... nnel-names