problem using BIOP vsi reader

[Aryeh Weiss]

I am trying  to help a colleague open his VSI files using ImageJ.
The file he sent me has a two parts:
Process_2297.vsi, which si 651kB in size.
_Process_2297_/stack1/frame_t_0_ets , which a 19.93GB in size.

When I run BIOP VSI reader, it comes up fine. I press "Select VSI" and
get the following two windows:

1. VSI Reader
This window contains data the macro needs. Please don't close it
Series ID :
/Users/amw1/Desktop/projects/itamarSimonCombing/shwarts/Process_2297.vsi
Image Folder : /Users/amw1/Desktop/projects/itamarSimonCombing/shwarts/
totSeries : 1
Has Label : No
Has Overview : No
Has Macro Image : No
Has Mask : No
Number Of Series : 0
Mode : Basic

2. Log
Relative Path, adding Path to Fiji
Full path to BIOPLib
:/Applications/local/fiji/Fiji.app/plugins/BIOP/BIOPLib.ijm
Empty Library. Adding BIOPLib Library.

I do not get the "Pick series" window which I found in the tutorial ppt  
presentation, in
http://biop.epfl.ch/downloads/VSIreader_tutov2.pdf

I have not been able to figure out how to display an image oy part of an
image.
I assume that I am missing something obvious, and any help in finding it
will be much appreciated.

--aryeh

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

Ph:  972-3-5317638
FAX: [phone]


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Romain Guiet]

Hi Aryeh,

thank you for your report.

Can you check a couple of thing.
1. Do you have the lastest LOCI Bio-formats installed? or the bio-formats update site activated ?
2. If you try, can you open your image (or a downscale version of it) using Bio-formats importer ?
3. Can you send us the informations you get from the windows Bio-formats Plugins Configuration -> Log

Can you provide us with a link to download your file so we can check that everything is fine with it ?

Cheers,

Romain




---------------------------------------------------------------
Dr. Romain Guiet
Bioimaging and Optics Platform (PT-BIOP)
Ecole Polytechnique Fédérale de Lausanne (EPFL)
Faculty of Life Sciences
Station 19, AI 0140
CH-1015 Lausanne

Phone: [+4121 69] 39629
http://biop.epfl.ch/
---------------------------------------------------------------

________________________________________
De : ImageJ Interest Group [[hidden email]] de la part de Aryeh Weiss [[hidden email]]
Envoyé : lundi 21 septembre 2015 15:40
À : [hidden email]
Objet : problem using BIOP vsi reader

I am trying  to help a colleague open his VSI files using ImageJ.
The file he sent me has a two parts:
Process_2297.vsi, which si 651kB in size.
_Process_2297_/stack1/frame_t_0_ets , which a 19.93GB in size.

When I run BIOP VSI reader, it comes up fine. I press "Select VSI" and
get the following two windows:

1. VSI Reader
This window contains data the macro needs. Please don't close it
Series ID :
/Users/amw1/Desktop/projects/itamarSimonCombing/shwarts/Process_2297.vsi
Image Folder : /Users/amw1/Desktop/projects/itamarSimonCombing/shwarts/
totSeries : 1
Has Label : No
Has Overview : No
Has Macro Image : No
Has Mask : No
Number Of Series : 0
Mode : Basic

2. Log
Relative Path, adding Path to Fiji
Full path to BIOPLib
:/Applications/local/fiji/Fiji.app/plugins/BIOP/BIOPLib.ijm
Empty Library. Adding BIOPLib Library.

I do not get the "Pick series" window which I found in the tutorial ppt
presentation, in
http://biop.epfl.ch/downloads/VSIreader_tutov2.pdf

I have not been able to figure out how to display an image oy part of an
image.
I assume that I am missing something obvious, and any help in finding it
will be much appreciated.

--aryeh

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

Ph:  972-3-5317638
FAX: [phone]


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Aryeh Weiss]

Hi Romain
Thank you for your reply.

On 9/22/15 10:13 AM, Romain Guiet wrote:
> Hi Aryeh,
>
> thank you for your report.
>
> Can you check a couple of thing.
> 1. Do you have the lastest LOCI Bio-formats installed? or the bio-formats update site activated ?
I have the bio-formats update site selected

> 2. If you try, can you open your image (or a downscale version of it) using Bio-formats importer ?
When I open it with the importer, I get a 512x300 x 6 image, which
appears to be thumbnails of the full images.  The image is not attached
to this version of the reply, so that it will go through the listserver.

> 3. Can you send us the informations you get from the windows Bio-formats Plugins Configuration -> Log
I can generate the log, but I cannot figure out how to copy what is in
the window. There are no menu items to do that, and highlight followed
by cmd-C does not work.

> Can you provide us with a link to download your file so we can check that everything is fine with it ?
This should work
https://filesender.huji.ac.il/filesender/?vid=37f1710c-1db5-3bc9-4a6e-0000619d7dcd

One other thing -- the action bar plugin causes Fiji (maybe also ImageJ
-- I dont know) to produce a grayed out help drop-down list.
This also happened in the past, so I have to dig up the bug report (or
file a new one).

Thank you for your help.
--aryeh

> Cheers,
>
> Romain
>
>
>
>
> ---------------------------------------------------------------
> Dr. Romain Guiet
> Bioimaging and Optics Platform (PT-BIOP)
> Ecole Polytechnique Fédérale de Lausanne (EPFL)
> Faculty of Life Sciences
> Station 19, AI 0140
> CH-1015 Lausanne
>
> Phone: [+4121 69] 39629
> http://biop.epfl.ch/
> ---------------------------------------------------------------
>
> ________________________________________
> De : ImageJ Interest Group [[hidden email]] de la part de Aryeh Weiss [[hidden email]]
> Envoyé : lundi 21 septembre 2015 15:40
> À : [hidden email]
> Objet : problem using BIOP vsi reader
>
> I am trying  to help a colleague open his VSI files using ImageJ.
> The file he sent me has a two parts:
> Process_2297.vsi, which si 651kB in size.
> _Process_2297_/stack1/frame_t_0_ets , which a 19.93GB in size.
>
> When I run BIOP VSI reader, it comes up fine. I press "Select VSI" and
> get the following two windows:
>
> 1. VSI Reader
> This window contains data the macro needs. Please don't close it
> Series ID :
> /Users/amw1/Desktop/projects/itamarSimonCombing/shwarts/Process_2297.vsi
> Image Folder : /Users/amw1/Desktop/projects/itamarSimonCombing/shwarts/
> totSeries : 1
> Has Label : No
> Has Overview : No
> Has Macro Image : No
> Has Mask : No
> Number Of Series : 0
> Mode : Basic
>
> 2. Log
> Relative Path, adding Path to Fiji
> Full path to BIOPLib
> :/Applications/local/fiji/Fiji.app/plugins/BIOP/BIOPLib.ijm
> Empty Library. Adding BIOPLib Library.
>
> I do not get the "Pick series" window which I found in the tutorial ppt
> presentation, in
> http://biop.epfl.ch/downloads/VSIreader_tutov2.pdf
>
> I have not been able to figure out how to display an image oy part of an
> image.
> I assume that I am missing something obvious, and any help in finding it
> will be much appreciated.
>
> --aryeh
>
> --
> Aryeh Weiss
> Faculty of Engineering
> Bar Ilan University
> Ramat Gan 52900 Israel
>
> Ph:  972-3-5317638
> FAX: [phone]
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

Ph:  972-3-5317638
FAX: [phone]

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Olivier Burri]

Hi All,

> > Can you provide us with a link to download your file so we can check that
> everything is fine with it ?
> This should work
> https://filesender.huji.ac.il/filesender/?vid=37f1710c-1db5-3bc9-4a6e-
> 0000619d7dcd

Thanks I got the file and modified the way the VSI reader searches for series in the file structure to include the current case.
If interested, we were using the fact that our "real" series contained the magnification used during acquisition (10x, 4x, etc...) and we used that to find them.

The image you provided did not have this string and thus caused the issue. Now we are using the fact that intermediate sizes contain a # character, while keeping previous functionality.

You can download the latest VSI reader through our update site.

> > 3. Can you send us the informations you get from the windows
> > Bio-formats Plugins Configuration -> Log
> I can generate the log, but I cannot figure out how to copy what is in the
> window. There are no menu items to do that, and highlight followed by cmd-
> C does not work.

Aah the beauty of the Mac, can't copy things from the Macro Recorder either... Thanks for trying.

> One other thing -- the action bar plugin causes Fiji (maybe also ImageJ
> -- I dont know) to produce a grayed out help drop-down list.
> This also happened in the past, so I have to dig up the bug report (or file a
> new one).

Check the latest actionBar version, at least on our PCs this element does not appear anymore since a little while...

Hope it will work for you now.

All the best

Oli

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Aryeh Weiss]

Hi Oli and thank you for your quick reply.

On 9/22/15 3:33 PM, Burri Olivier wrote:

> Hi All,
>
>>> Can you provide us with a link to download your file so we can check that
>> everything is fine with it ?
>> This should work
>> https://filesender.huji.ac.il/filesender/?vid=37f1710c-1db5-3bc9-4a6e-
>> 0000619d7dcd
> Thanks I got the file and modified the way the VSI reader searches for series in the file structure to include the current case.
> If interested, we were using the fact that our "real" series contained the magnification used during acquisition (10x, 4x, etc...) and we used that to find them.
>
> The image you provided did not have this string and thus caused the issue. Now we are using the fact that intermediate sizes contain a # character, while keeping previous functionality.
>
> You can download the latest VSI reader through our update site.

I updated and indeed it now finds hte series. However, when I select
"small" thumbnails and tryto continue, it pops up a window
that says "Macro error", and the Log window shas the following:

java.lang.reflect.InvocationTargetException
     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
     at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
     at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
     at java.lang.reflect.Method.invoke(Method.java:597)
     at
loci.plugins.macro.MacroFunctions.handleExtension(MacroFunctions.java:82)
     at ij.macro.ExtensionDescriptor.dispatch(ExtensionDescriptor.java:288)
     at ij.macro.Functions.doExt(Functions.java:4445)
     at ij.macro.Functions.getStringFunction(Functions.java:274)
and a lot more....

>>> 3. Can you send us the informations you get from the windows
>>> Bio-formats Plugins Configuration -> Log
>> I can generate the log, but I cannot figure out how to copy what is in the
>> window. There are no menu items to do that, and highlight followed by cmd-
>> C does not work.
> Aah the beauty of the Mac, can't copy things from the Macro Recorder either... Thanks for trying.
>
>> One other thing -- the action bar plugin causes Fiji (maybe also ImageJ
>> -- I dont know) to produce a grayed out help drop-down list.
>> This also happened in the past, so I have to dig up the bug report (or file a
>> new one).
> Check the latest actionBar version, at least on our PCs this element does not appear anymore since a little while...

I use the update site, so I should have the latest version.

> Hope it will work for you now.
>
> All the best
>
> Oli
>

Many thanks.
--aryeh

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

Ph:  972-3-5317638
FAX: [phone]

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html