[ome-devel] BF does not open some .stk file correctly

[Roger Leigh]

Thanks.  I've opened a ticket for this:
http://trac.openmicroscopy.org.uk/ome/ticket/12503
You should be CCd on it.


Regards,
Roger

On 30/07/14 13:38, Hadrien Mary wrote:
> In fact I have checked axes order with tifffile.py so it may not be the
> same order as BF. However it does not matter here because I know these
> file does not contain Z axes (only T) from metamorph. So I think BF
> detect T=5 and Z=2 while it should detect T=10 and Z=1.

> On Wed, Jul 30, 2014 at 12:13 PM, Roger Leigh <rleigh at dundee.ac.uk
> <mailto:rleigh at dundee.ac.uk>> wrote:
>
>     On 29/07/14 14:03, Hadrien Mary wrote:
>
>         Hi,
>
>         I may have a bug with some .stk file. I paste here the bug from
>         Fiji Bugzilla:
>
>         ****
>         Note that I use a recent IJ/Fiji version (and the bug has also been
>         noticed with an older IJ version few months ago).
>
>         Some .stk files are not correctly detected by BF and IJ open
>         them with
>         two axes (Z and T) while only one exist. Examples (axes order is
>         T, Z,
>         X, Y, C) :
>
>         - file1.stk : real shape = (10, 1, 264, 268, 1), BF detected
>         shape = (5,
>         2, 264, 268, 1)
>
>
>     Current dev_5_0:
>
>              Width = 268
>              Height = 264
>              SizeZ = 2
>              SizeT = 5
>              SizeC = 1
>
>
>         - file2.stk (with several channels): real shape = (10, 1, 139,
>         224, 3),
>         BF detected shape = (5, 2, 139, 224, 3)
>
>
>              Width = 224
>              Height = 139
>              SizeZ = 2
>              SizeT = 5
>              SizeC = 3 (effectively 1)
>
>
>         Both files have been saved from Metamorph after a z-projection
>         (I bet
>         the issue comes from here).
>
>         They open well on different Metamorph versions and also
>         tifffile.py lib
>         detects the correct shapes.
>
>         Both stk are in the attachment file called stk_files.zip
>         ***
>
>         Original bug can be found here :
>         http://fiji.sc/bugzilla/show___bug.cgi?id=868
>         <http://fiji.sc/bugzilla/show_bug.cgi?id=868> (it has been
>         closed since it
>         seems to be a bug only related to BF).
>
>         You can find attachment file on the Fiji Bugzilla.
>
>
>     Thanks.  Just to double check your figures above, are the X and Y
>     transposed; the TIFF data and Bio-Formats show them to be the other way
>     around.  Are all the other dimensions correct in the axes order above?


--
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