names of channels with lif format

[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

[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

[sameh]

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

[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

[sameh]

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 !

[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