[ome-users] ome-users Digest, Vol 119, Issue 5

[Roger Leigh]

On 20/02/15 14:41, ImageJ wrote:
> 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) #1Leica/DAPI
> Rat-6div-TIV-488-AP3-CY3-MAP2 HardwareSetting|FilterSettingRecord|SP
> Mirror Channel 2 (left) #1495.324675324675
> Rat-6div-TIV-488-AP3-CY3-MAP2 HardwareSetting|FilterSettingRecord|SP
> Mirror Channel 2 (right) #1553.116883116883
> Rat-6div-TIV-488-AP3-CY3-MAP2 HardwareSetting|FilterSettingRecord|SP
> Mirror Channel 2 (stain) #1Leica/ALEXA 488
> Rat-6div-TIV-488-AP3-CY3-MAP2 HardwareSetting|FilterSettingRecord|SP
> Mirror Channel 3 (left) #1570
> Rat-6div-TIV-488-AP3-CY3-MAP2 HardwareSetting|FilterSettingRecord|SP
> Mirror Channel 3 (right) #1627.012987012987
> Rat-6div-TIV-488-AP3-CY3-MAP2 HardwareSetting|FilterSettingRecord|SP
> Mirror Channel 3 (stain) #1Leica/Cy3
> Rat-6div-TIV-488-AP3-CY3-MAP2 HardwareSetting|FilterSettingRecord|SP
> Mirror Channel 4 (left) #1650
> Rat-6div-TIV-488-AP3-CY3-MAP2 HardwareSetting|FilterSettingRecord|SP
> Mirror Channel 4 (right) #1750
> Rat-6div-TIV-488-AP3-CY3-MAP2 HardwareSetting|FilterSettingRecord|SP
> Mirror Channel 4 (stain) #1Leica/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 ?

 From what I can tell, the metadata is correct, but the image order is
reversed.  I can certainly reproduce it with showinf, ImageJ and ICY.  I
have opened a ticket for this and CCd you on it:

   https://trac.openmicroscopy.org/ome/ticket/12756#ticket


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