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

[Aryeh Weiss]

Hi Melissa

Thank you for your reply.

On 05/10/2015 12:38 AM, Melissa Linkert wrote:
> Hi Aryeh,
>
>> Thank you for your reply. I the permissions listed below. The
>> filename had been changed to Test.vsi and _Test_
> Just to make certain - the .vsi name is definitely "Test.vsi"?
> I would expect to see this problem if there is any difference between
> the file name without ".vsi" and the folder name without the two "_"
> (even something like "test.vsi" vs. "_Test_" would be a problem).
>
>>> 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
> That all seems fine.  The next two things to try are:
>
> 1) Try opening the .ets file - I would expect that to show an error
> message, but the contents of the error message should help to identify
> the problem.
>
> 2) Select "Plugins > Bio-Formats > Bio-Formats Plugins Configuration",
> then choose "CellSens VSI" from the list in the "Formats" tab.  Verify
> that the "Enabled" box is checked - it should be checked by default, but
> I can reproduce the problem that you describe when that box is not checked.

2) was the problem after enabling Cellsens VSI all is well.
Since the vsi file opened, it did not occur to me that this might be the 
problem -- sorry about that
> Regards,
> -Melissa
Best regards
--aryeh
>
> On Wed, Sep 30, 2015 at 06:38:06PM +0300, Aryeh Weiss wrote:
>> 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
>>>>
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-- 
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

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