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

Sun Oct 4 22:38:25 BST 2015

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.

Regards,
-Melissa

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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> >
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> >
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