[ome-users] ome-users Digest, Vol 119, Issue 5
ImageJ
imagejlyd at gmail.com
Fri Feb 20 14:41:15 GMT 2015
Dear Roger,
I uploaded my lif file on the provides link.
The name was the following:
Manipdu01-12-2014.lif
I also added a text file with the description of the problem, which are the following:
The metadata that I could load on fiji are the following:
Rat-6div-TIV-488-AP3-CY3-MAP2 HardwareSetting|FilterSettingRecord|SP Mirror Channel 1 (stain) #1 Leica/DAPI
Rat-6div-TIV-488-AP3-CY3-MAP2 HardwareSetting|FilterSettingRecord|SP Mirror Channel 2 (left) #1 495.324675324675
Rat-6div-TIV-488-AP3-CY3-MAP2 HardwareSetting|FilterSettingRecord|SP Mirror Channel 2 (right) #1 553.116883116883
Rat-6div-TIV-488-AP3-CY3-MAP2 HardwareSetting|FilterSettingRecord|SP Mirror Channel 2 (stain) #1 Leica/ALEXA 488
Rat-6div-TIV-488-AP3-CY3-MAP2 HardwareSetting|FilterSettingRecord|SP Mirror Channel 3 (left) #1 570
Rat-6div-TIV-488-AP3-CY3-MAP2 HardwareSetting|FilterSettingRecord|SP Mirror Channel 3 (right) #1 627.012987012987
Rat-6div-TIV-488-AP3-CY3-MAP2 HardwareSetting|FilterSettingRecord|SP Mirror Channel 3 (stain) #1 Leica/Cy3
Rat-6div-TIV-488-AP3-CY3-MAP2 HardwareSetting|FilterSettingRecord|SP Mirror Channel 4 (left) #1 650
Rat-6div-TIV-488-AP3-CY3-MAP2 HardwareSetting|FilterSettingRecord|SP Mirror Channel 4 (right) #1 750
Rat-6div-TIV-488-AP3-CY3-MAP2 HardwareSetting|FilterSettingRecord|SP Mirror Channel 4 (stain) #1 Leica/Cy5
However the picture are loaded in this order in FIJI:
Channel1: Leica/Cy5
Channel2: Leica/CY3
Channel3: Leica/ALEXA 488
Channel4: Leica/DAPI
The picture are loaded in the same order in ICY:
Channel1: Leica/Cy5
Channel2: Leica/CY3
Channel3: Leica/ALEXA 488
Channel4: Leica/DAPI
And ICY displays that names:
Channel 1 : Leica/DAPI
Channel 2: Leica/ALEXA 488
Channel3: Leica/Cy3
Channel4: Leica/Cy5
So it seems that the channel name are conserved but not the channel order.
Could you find a solution ?
Thanks a lot.
Lydia.
Le 4 févr. 2015 à 13:00, ome-users-request at lists.openmicroscopy.org.uk a écrit :
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> Today's Topics:
>
> 1. Re: Lif channel name in bioformat (Roger Leigh)
> 2. Re: Unable to move project from one group to an other
> (Mark Carroll (Staff))
> 3. Re: Unable to move project from one group to an other
> (Philippe Mailly)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 4 Feb 2015 09:44:49 +0000
> From: Roger Leigh <rleigh at dundee.ac.uk>
> To: <ome-users at lists.openmicroscopy.org.uk>
> Subject: Re: [ome-users] Lif channel name in bioformat
> Message-ID: <54D1EA11.9070606 at dundee.ac.uk>
> Content-Type: text/plain; charset="windows-1252"; format=flowed
>
> On 03/02/15 20:22, ImageJLyd wrote:
>
>> I'm currently working with lif files generated on a Leica SP5 confocal
>> microscope.
>> I would like to warn you about the fact that the channel names are wrong
>> when opening .lif file with Icy software.
>> Channel names :
>> channel 1 is wrongly indicating the name of the channel 4
>> Channel 2 is wrongly indicating the name of the channel 3
>> Channel 3 is wrongly indicating the name of the channel 2
>> Channel 4 is wrongly indicating the name of the channel 1
>>
>> When I read the metadata of the lif file in Fiji, it appears,that
>> actually even if LUT are respected in fiji (and not in icy), the channel
>> names are inverted in comparison with leica software. Could it come from
>> the bioformat ?
>
> If you could possibly upload an example file which is showing the
> problem using:
>
> http://qa.openmicroscopy.org.uk/qa/upload/
>
> then we can take a look at it and provide an answer to your question,
> and if there's a problem we can look into what might need fixing.
>
>
> Kind regards,
> Roger
>
> --
> Dr Roger Leigh -- Open Microscopy Environment
> Wellcome Trust Centre for Gene Regulation and Expression,
> College of Life Sciences, University of Dundee, Dow Street,
> Dundee DD1 5EH Scotland UK Tel: (01382) 386364
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 4 Feb 2015 10:56:38 +0000
> From: "Mark Carroll (Staff)" <m.t.b.carroll at dundee.ac.uk>
> To: "ome-users at lists.openmicroscopy.org.uk"
> <ome-users at lists.openmicroscopy.org.uk>
> Subject: Re: [ome-users] Unable to move project from one group to an
> other
> Message-ID: <1423047397214.36726 at dundee.ac.uk>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Philippe,
>
>> However, this image (10000) is only in this dataset, I get only one row ??
>
> Yes, it does seem so. I don't suppose it is possible that the dataset could be in multiple projects?
>
> bin/omero hql "select parent from ProjectDatasetLink where child = 736"
>
> Cheers,
>
> Mark
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 04 Feb 2015 12:42:43 +0100
> From: Philippe Mailly <philippe.mailly at college-de-france.fr>
> To: OME User Support List <ome-users at lists.openmicroscopy.org.uk>
> Subject: Re: [ome-users] Unable to move project from one group to an
> other
> Message-ID: <54D205B3.5040800 at college-de-france.fr>
> Content-Type: text/plain; charset="windows-1252"; Format="flowed"
>
> Hi Mark,
>
> Finally, I remove the dataset and transfer the data to the good location.
>
>
> Philippe
>
> Le 04/02/2015 11:56, Mark Carroll (Staff) a ?crit :
>> Dear Philippe,
>>
>>> However, this image (10000) is only in this dataset, I get only one row ??
>> Yes, it does seem so. I don't suppose it is possible that the dataset could be in multiple projects?
>>
>> bin/omero hql "select parent from ProjectDatasetLink where child = 736"
>>
>> Cheers,
>>
>> Mark
>>
>> The University of Dundee is a registered Scottish Charity, No: SC015096
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
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