[ome-users] Leica .lif import of stacks from tile scanning

Melissa Linkert melissa at glencoesoftware.com
Thu May 16 01:21:03 BST 2013 

Hi Glen,

> Thanks. But, that didn't do it . Given 2 stacks of 2D time-lapse with 2 channels and n images;  the group files option interleaved the 2 stacks to create a 2-channel stack with 2 z-planes and n images.  
> 

Yes, that is what I would expect to happen.  If you actually want the
end result to be 2 channels with n x 2 timepoints, then the easiest
thing to do is change the "Slices (z)" and "Frames (t)" values in the
image properties window.  The "Group files with similar names" option
does not do that by default as it is trying to preserve what looks like
the Z section indices being encoded in the filename.

Regards,
-Melissa

On Thu, May 16, 2013 at 07:56:33AM +0800, Glen MacDonald wrote:
> Thanks. But, that didn't do it . Given 2 stacks of 2D time-lapse with 2 channels and n images;  the group files option interleaved the 2 stacks to create a 2-channel stack with 2 z-planes and n images.  
> 
> regards,
> Glen MacDonald
> 	Core for Communication Research
> Virginia Merrill Bloedel Hearing Research Center
> 	Cellular Morphology Core
> Center on Human Development and Disability
> Box 357923
> University of Washington
> Seattle, WA 98195-7923  USA
> (206) 616-4156
> glenmac at uw.edu
> 
> 
> 
> 
> 
> 
> 
> On May 15, 2013, at 8:33 PM, Melissa Linkert <melissa at glencoesoftware.com> wrote:
> 
> > Hi Glen,
> > 
> >> LOCI has an option to 'Concatenate series when compatible'.  What file naming conventions are required for this to function?  I have 2 time-lapse series - 'zebrafish01_1.ome' and 'zebrafish01_2.ome' in the same directory.  If selected, should this option recognize and merge those 2 images?
> >> 
> > 
> > The "Concatenate series when compatible" option does not group together
> > different files; probably you would want to use the "Group files with
> > similar names" option instead.
> > 
> > The file naming requirements are fairly flexible.  In general, as long
> > as the names are the same except for one or more numbers, the files will
> > be automatically detected as belonging together; 'zebrafish01_1.ome'
> > and 'zebrafish01_2.ome' should definitely work.  There is also an option
> > to specify exactly which files belong together, if automatic detection
> > does not work.
> > 
> > See this section of the Bio-Formats documentation for more information:
> > 
> > http://www.openmicroscopy.org/site/support/bio-formats/users/imagej/load-images.html#group-files-with-similar-names
> > 
> > Regards,
> > -Melissa
> > 
> > On Wed, May 15, 2013 at 02:29:29PM +0800, Glen MacDonald wrote:
> >> Hello,
> >> LOCI has an option to 'Concatenate series when compatible'.  What file naming conventions are required for this to function?  I have 2 time-lapse series - 'zebrafish01_1.ome' and 'zebrafish01_2.ome' in the same directory.  If selected, should this option recognize and merge those 2 images?
> >> 
> >> Regards
> >> Glen MacDonald
> >> 	Core for Communication Research
> >> Virginia Merrill Bloedel Hearing Research Center
> >> 	Cellular Morphology Core
> >> Center on Human Development and Disability
> >> Box 357923
> >> University of Washington
> >> Seattle, WA 98195-7923  USA
> >> (206) 616-4156
> >> glenmac at uw.edu
> >> 
> >> 
> >> 
> >> 
> >> 
> >> 
> >> 
> >> On May 15, 2013, at 6:23 AM, Melissa Linkert <melissa at glencoesoftware.com> wrote:
> >> 
> >>> Hi Kai,
> >>> 
> >>>> I did not have a response from you to my recent reply. 
> >>> 
> >>> My apologies for the delay.
> >>> 
> >>>> All I really need to know is whether the behaviour of Bio-Formats for Leica imports is going to change or not. I spent a lot of time writing my macro to import and tile stitch Leica data. Now that my macro is ready, the Bio-Formats importer has changed and does not import Leica stacks as stacks any more (even with "Concatenate when compatible" ticked). I can edit my macro to adapt to this new behaviour, but investing this work would make little sense if you are going to correct the behaviour of Bio-Formats.
> >>>> 
> >>> 
> >>> The current behavior is correct, and will not change.  The previous
> >>> behavior was incorrect, as it meant that all tiles and timepoints were
> >>> treated the same; for example, if you had 5 tiles with 2 timepoints, it would
> >>> appear as though there were 10 timepoints.
> >>> 
> >>> As long as everything selected has the exact same dimensions, "Concatenate
> >>> when compatible" really should work.  If you try to open multiple sets of tiles
> >>> with different dimensions all at once, then "Concatenate when
> >>> compatible" will not work.  I would guess that your macro could
> >>> automatically select which tiles to open together based upon the image
> >>> names, but without knowing what your data looks like I can't say for sure.
> >>> 
> >>> Regards,
> >>> -Melissa
> >>> 
> >>> On Tue, May 14, 2013 at 01:21:37PM +0100, Kai Toellner wrote:
> >>>> Dear Melissa,
> >>>> 
> >>>> I did not have a response from you to my recent reply. 
> >>>> All I really need to know is whether the behaviour of Bio-Formats for Leica imports is going to change or not. I spent a lot of time writing my macro to import and tile stitch Leica data. Now that my macro is ready, the Bio-Formats importer has changed and does not import Leica stacks as stacks any more (even with "Concatenate when compatible" ticked). I can edit my macro to adapt to this new behaviour, but investing this work would make little sense if you are going to correct the behaviour of Bio-Formats.
> >>>> 
> >>>> Kind regards,
> >>>> 
> >>>> Kai
> >>>> 
> >>>> 
> >>>> -----Original Message-----
> >>>> From: Kai Toellner 
> >>>> Sent: 09 May 2013 22:50
> >>>> To: 'melissa at glencoesoftware.com'
> >>>> Subject: RE: [ome-users] Leica .lif import of stacks from tile scanning
> >>>> 
> >>>> Dear Melissa,
> >>>> 
> >>>> Thank you for the prompt reply.
> >>>> 
> >>>> The new behaviour started for me sometime this week. My version of Fiji has been updated over the last few weeks on an almost daily basis. I still have one Fiji version on a Mac computer that has not been updated for some time and still shows the old behaviour. This version presents itself as vers. 4.5-DEV from 18th March 2013.
> >>>> 
> >>>> I tried the "Concatenate when compatible" option. Unfortunately this does not change the behaviour for the Leica .lif files I am trying to read. 
> >>>> 
> >>>> I am not sure what the advantage is of showing each tile as an individual series. This means that I need to do 60 clicks to open a dataset of 60 tiles, whereas until last week I could choose one dataset with one single click. Is there still a way to do this?
> >>>> 
> >>>> Regards,
> >>>> Kai
> >>>> 
> >>>> -----Original Message-----
> >>>> From: Melissa Linkert [mailto:melissa.linkert at gmail.com] On Behalf Of Melissa Linkert
> >>>> Sent: 08 May 2013 23:20
> >>>> To: Kai Toellner
> >>>> Cc: ome-users at lists.openmicroscopy.org.uk
> >>>> Subject: Re: [ome-users] Leica .lif import of stacks from tile scanning
> >>>> 
> >>>> Hi Kai,
> >>>> 
> >>>>> I am importing stacks of four channel (4C) tile scans from a Leica microscope, written as .lif files, into Fiji. Fiji is automatically updating and just updated Loci bioformats to vers. 4.4.9-DEV rev 34f3393, built 7 May 13. Imagej is vers. 1.47q. The problem I describe is reproducible under Windows and iOS.
> >>>>> Before the update different stacks of 4C tile scans were each showing as individual images (series) on the second page of the bio-formats plugin (Choose series). To import the whole stack I had to only select one series.
> >>>>> Since the most recent update all tiles of the tile scan show as individual series, meaning to import the whole stack I have to mark and import all individual images, which results in the import of dozens of individual images, not one single stack.
> >>>>> This upsets a macro I have just written that relies on the import of a stack of tiles, not many separate tiles.
> >>>>> Question: Is this a bug of the latest version of bioformats and will be fixed at some stage, or is this a new feature that will stay permanently?
> >>>>> 
> >>>> 
> >>>> This is the expected behavior, and was introduced in the 4.4.7 version of Bio-Formats.  Including the tiles in the stack caused problems for anyone who had timelapse tile scans, in addition to preventing the stitching plugins in Fiji from being able to stitch the tiles.
> >>>> 
> >>>> The "Concatenate series when compatible" option should collapse all of the selected tiles back into a single stack.
> >>>> 
> >>>> Regards,
> >>>> -Melissa
> >>>> 
> >>>> On Wed, May 08, 2013 at 03:14:06PM +0100, Kai Toellner wrote:
> >>>>> I am importing stacks of four channel (4C) tile scans from a Leica microscope, written as .lif files, into Fiji. Fiji is automatically updating and just updated Loci bioformats to vers. 4.4.9-DEV rev 34f3393, built 7 May 13. Imagej is vers. 1.47q. The problem I describe is reproducible under Windows and iOS.
> >>>>> Before the update different stacks of 4C tile scans were each showing as individual images (series) on the second page of the bio-formats plugin (Choose series). To import the whole stack I had to only select one series.
> >>>>> Since the most recent update all tiles of the tile scan show as individual series, meaning to import the whole stack I have to mark and import all individual images, which results in the import of dozens of individual images, not one single stack.
> >>>>> This upsets a macro I have just written that relies on the import of a stack of tiles, not many separate tiles.
> >>>>> Question: Is this a bug of the latest version of bioformats and will be fixed at some stage, or is this a new feature that will stay permanently?
> >>>>> 
> >>>>> Kai
> >>>>> 
> >>>>> Dr. Kai-Michael Toellner
> >>>>> Senior Research Fellow
> >>>>> School of Immunity and Infection
> >>>>> Institute for Biomedical Research (IBR) room 432 Medical School 
> >>>>> University of Birmingham Birmingham B15 2TT United Kingdom
> >>>>> Tel: +44 121 41 58687
> >>>>> FAX: +44 121 41 43599
> >>>>> 
> >>>> 
> >>>>> _______________________________________________
> >>>>> ome-users mailing list
> >>>>> ome-users at lists.openmicroscopy.org.uk
> >>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >>>> 
> >>> _______________________________________________
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> >> 
>

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