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

[Melissa Linkert]

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
> 

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