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

[Hadrien Mary]

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.


--
Hadrien Mary

Ph.D student in Biology
Tournier-Gachet Team
CNRS - LBCMCP - UMR 5088

Université de Toulouse - Bât. 4R3B1
118, route de Narbonne - 31062 Toulouse


On Wed, Jul 30, 2014 at 12:13 PM, Roger Leigh <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 (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
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