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

[Roger Leigh]

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 (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?



Thanks,
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