[ome-users] bio-formats problem opening a VSI image set

[Aryeh Weiss]

Thank you for your reply. I the permissions listed below. The filename 
had been changed to Test.vsi and _Test_
.

The structure is
_Test_/stack1/ frame_t_0.ets

On 9/30/15 6:07 PM, Balaji Ramalingam (Staff) wrote:
> Hi,
>
> Testing locally on OSX, we were able to open the ³.vsi" along with the
> corresponding ".ets" file in ImageJ(using the latest version of BF).
> The only issue that we could think of in your case, could be the
> permissions on the files.
> Could you please check if both the ³.vsi" and ".ets" files have read
> permissions?
>
> It would help us troubleshoot the issue better, if you could paste the
> output of : ls -ahl (on the parent directory).

amw1 itamarSimonCombing $ ls -ahl _Test_
total 16
drwxrwxrwx  4 amw1  staff   136B Sep 30 18:32 .
drwxr-xr-x  9 amw1  staff   306B Sep 24 14:48 ..
-rwxrwxrwx@ 1 amw1  staff   6.0K Sep 24 14:45 .DS_Store
drwxrwxrwx  3 amw1  staff   102B Sep 21 16:00 stack1

and

amw1 _Test_ $ ls -ahl stack1
total 38925512
drwxrwxrwx  3 amw1  staff   102B Sep 21 16:00 .
drwxrwxrwx  4 amw1  staff   136B Sep 30 18:32 ..
-rwxrwxrwx  1 amw1  staff    19G Aug 27 13:22 frame_t_0.ets

Best regards
--aryeh

-- 
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: 972-3-7384051


>
>
>
> On 29/09/2015 17:44, "Aryeh Weiss" <aryeh at cc.huji.ac.il> wrote:
>
>> I have a VSI file that is not being read correctly by bio-formats. I
>> discovered this when trying to use the VSI reader.
>> It works correctly on a Windows 7 system, so this may be OSX specific.
>> The problem occurs on both Java 1.6.0_65 and Java 1.8.0_60.
>>
>> There is no error generated, but the bio-formats importer only opens the
>> smallest image (which is stored in Process_2297.vsi).
>> It fails to related to the images in the
>> _Process_2297_>stack1>frame_t_0.ets file (which is almost 20GB big and
>> has the rest of the images.
>> I worked with Oli Burri to verify that the file is valid and works for
>> him. It also works on his mac, so you not be able to reproduce the
>> problem, but we can only hope... On Oli's computer, the importer will
>> show a list of series (which are images at increasing resolution).
>>
>> The zip file is still 14+ GB , so I cannot upload it from home, but the
>> following link should work:
>> https://filesender.huji.ac.il/filesender/?vid=37f1710c-1db5-3bc9-4a6e-0000
>> 619d7dcd
>> The image will have a different name (I had remnai
>>
>> I tried it also with a new installation of Fiji, and reproduced the error.
>>
>> Also, I made sure that I have the latest bio-formats and loci (though
>> the update sites).
>>
>> Any help you can provide will be most appreciated.
>>
>> --aryeh
>>
>> --
>> Aryeh Weiss
>> Faculty of Engineering
>> Bar Ilan University
>> Ramat Gan 52900 Israel
>>
>> Ph:  972-3-5317638
>> FAX: 972-3-7384051
>>
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
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>
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