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

[Hadrien Mary]

I use BF 5.0.2 and I just checked with BF package daily build and I obtain
the same result as before.


--
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 2:38 PM, Hadrien Mary <hadrien.mary at gmail.com>
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.
>
>
> --
> 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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>>
>
>
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