Loci bug opening Aperio svs file

[Serena Buscone]

Hi all, i work with fluorescence whole slide images obtained with an Aperio Scanner. I tried to open those svs files in imageJ and Fiji with LOCI plugin but it doesn't work. Some one can suggest me how to solve this problem ?
Thank you very much

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

[ctrueden]

Hi Serena,

Thanks for the bug report.

[CCing the ome-users list, which is the best place to discuss Bio-Formats
issues.]

> Hi all, i work with fluorescence whole slide images obtained with an
> Aperio Scanner. I tried to open those svs files in imageJ and Fiji
> with LOCI plugin but it doesn't work. Some one can suggest me how to
> solve this problem ?

Could you please upload a sample non-working SVS file? It would help us
diagnose and fix the problem.

If file is 500 MB or less, you can use:
http://qa.openmicroscopy.org.uk/qa/upload/

Or if larger, let us know and we will send you FTP server credentials
off-list.

Thanks,
Curtis


On Thu, Jun 20, 2013 at 4:58 AM, Serena Buscone <[hidden email]>wrote:

> Hi all, i work with fluorescence whole slide images obtained with an
> Aperio Scanner. I tried to open those svs files in imageJ and Fiji with
> LOCI plugin but it doesn't work. Some one can suggest me how to solve this
> problem ?
> Thank you very much
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Melissa Linkert-2]

Hi Serena,

> > Hi all, i work with fluorescence whole slide images obtained with an
> > Aperio Scanner. I tried to open those svs files in imageJ and Fiji
> > with LOCI plugin but it doesn't work. Some one can suggest me how to
> > solve this problem ?

Note that if you are seeing an error message similar to
"OutOfMemoryError" or "NegativeArraySizeException", then you will almost
certainly need to open a smaller section of the image(s) by using the
"Crop on import" option in the "Bio-Formats Import Options" window.  SVS
files typically contain very large images which cannot be displayed all
at once.

If you are able to open sections of the image using "Crop on import",
then there is no need to send the file.  If you see a different error
message and/or "Crop on import" does not solve the problem, then please
send one of your files as indicated by Curtis, along with the error
message that you are seeing.

Regards,
-Melissa

On Thu, Jun 20, 2013 at 11:35:15AM -0500, Curtis Rueden wrote:

> Hi Serena,
>
> Thanks for the bug report.
>
> [CCing the ome-users list, which is the best place to discuss Bio-Formats
> issues.]
>
> > Hi all, i work with fluorescence whole slide images obtained with an
> > Aperio Scanner. I tried to open those svs files in imageJ and Fiji
> > with LOCI plugin but it doesn't work. Some one can suggest me how to
> > solve this problem ?
>
> Could you please upload a sample non-working SVS file? It would help us
> diagnose and fix the problem.
>
> If file is 500 MB or less, you can use:
> http://qa.openmicroscopy.org.uk/qa/upload/
>
> Or if larger, let us know and we will send you FTP server credentials
> off-list.
>
> Thanks,
> Curtis
>
>
> On Thu, Jun 20, 2013 at 4:58 AM, Serena Buscone <[hidden email]>wrote:
>
> > Hi all, i work with fluorescence whole slide images obtained with an
> > Aperio Scanner. I tried to open those svs files in imageJ and Fiji with
> > LOCI plugin but it doesn't work. Some one can suggest me how to solve this
> > problem ?
> > Thank you very much
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >

> _______________________________________________
> ome-users mailing list
> [hidden email]
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users

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

[Vitali Khvatkov-2]

Serena,
Aperio SVS is a Whole Slide Image or "Digital Slide" that has tiled
pyramid organization based on BigTiff format. Your options depend on
your definition of "work"

- If you need to just view Aperio SVS file on local computer, Aperio has
free download desktop viewer called ImageScope
http://www.aperio.com/appcenter

- If you need to annotate, measure or share this image with multiple
users you can create free account on our  public server and upload SVS
slides there http://host.simagis.com/live/register

- If you need to run quantitative analysis on the whole slide image, you
are getting into area of High Performance Computing. Desktop software is
usually not suitable this task. Our servers provide functionality to run
ImageJ macros on whole slide images but we only allow this feature on
private servers due to security and resource constraints.

--
Vitali Khvatkov
Smart Imaging Technologies Co.
live.simagis.com



Serena Buscone wrote:
> Hi all, i work with fluorescence whole slide images obtained with an Aperio Scanner. I tried to open those svs files in imageJ and Fiji with LOCI plugin but it doesn't work. Some one can suggest me how to solve this problem ?
> Thank you very much
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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

[ctrueden]

Hi Vitali,

> If you need to run quantitative analysis on the whole slide image, you
> are getting into area of High Performance Computing. Desktop software
> is usually not suitable this task. Our servers provide functionality
> to run ImageJ macros on whole slide images but we only allow this
> feature on private servers due to security and resource constraints.

On the contrary, ImageJ absolutely *can* do such quantitative analysis.
Desktop computers are really powerful these days, and ImageJ (especially
with its scripting capabilities) is very adaptable to these sorts of
projects.

That said, I agree with you that running analysis on a high-performance
server cluster such as yours can be much, much faster, depending on the
quantity of data and what you are trying to do. But I don't think it's fair
to say that desktops are "not suitable" in most cases.

Regards,
Curtis


On Thu, Jun 20, 2013 at 12:16 PM, Vitali Khvatkov <
[hidden email]> wrote:

> Serena,
> Aperio SVS is a Whole Slide Image or "Digital Slide" that has tiled
> pyramid organization based on BigTiff format. Your options depend on your
> definition of "work"
>
> - If you need to just view Aperio SVS file on local computer, Aperio has
> free download desktop viewer called ImageScope http://www.aperio.com/**
> appcenter <http://www.aperio.com/appcenter>
>
> - If you need to annotate, measure or share this image with multiple users
> you can create free account on our  public server and upload SVS slides
> there http://host.simagis.com/live/**register<http://host.simagis.com/live/register>
>
> - If you need to run quantitative analysis on the whole slide image, you
> are getting into area of High Performance Computing. Desktop software is
> usually not suitable this task. Our servers provide functionality to run
> ImageJ macros on whole slide images but we only allow this feature on
> private servers due to security and resource constraints.
>
> --
> Vitali Khvatkov
> Smart Imaging Technologies Co.
> live.simagis.com
>
>
>
>
> Serena Buscone wrote:
>
>> Hi all, i work with fluorescence whole slide images obtained with an
>> Aperio Scanner. I tried to open those svs files in imageJ and Fiji with
>> LOCI plugin but it doesn't work. Some one can suggest me how to solve this
>> problem ?
>> Thank you very much
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>

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

[Serena Buscone]

Hi Curtis,
thank you very much for your answer,  i tried to upload the images in omero
but because i can't find find the svs file format in the list i can't
upload them.
I can change the file format in TIFF one but without compression each image
become larger than 2 GB.
Maby using the FTP server should be easier to upload svs files.

Thanks for your collaboration
Serena



2013/6/20 Curtis Rueden <[hidden email]>

> Hi Serena,
>
> Thanks for the bug report.
>
> [CCing the ome-users list, which is the best place to discuss Bio-Formats
> issues.]
>
> > Hi all, i work with fluorescence whole slide images obtained with an
> > Aperio Scanner. I tried to open those svs files in imageJ and Fiji
> > with LOCI plugin but it doesn't work. Some one can suggest me how to
> > solve this problem ?
>
> Could you please upload a sample non-working SVS file? It would help us
> diagnose and fix the problem.
>
> If file is 500 MB or less, you can use:
> http://qa.openmicroscopy.org.uk/qa/upload/
>
> Or if larger, let us know and we will send you FTP server credentials
> off-list.
>
> Thanks,
> Curtis
>
>
> On Thu, Jun 20, 2013 at 4:58 AM, Serena Buscone <[hidden email]
> >wrote:
>
> > Hi all, i work with fluorescence whole slide images obtained with an
> > Aperio Scanner. I tried to open those svs files in imageJ and Fiji with
> > LOCI plugin but it doesn't work. Some one can suggest me how to solve
> this
> > problem ?
> > Thank you very much
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Vitali Khvatkov-2]

Perhaps the following information may help:

Aperio SVS File is format with complex internal organization, it is
created for Digital Pathology applications.
It contains what is called tiled image pyramid, see illustration
http://climserv.ipsl.polytechnique.fr/documentation/idl_help/images/img_pyrm.gif 

This data structure is designed to enable fast viewing of the image *by
special programs* , that can access just a portion of the image at a
time, without loading whole image to computer memory.

Yes, this structure is compatible with TIFF (BigTiff version) you even
rename SVS to tiff and open it with TIFF viewer (if file is small that is)
But  to access tiled pyramid correctly (without loading it to memory)
you need special viewer.

Compression is another problem: Your digital slide may be compressed
with JPEG compression at 30:1 ratio , but if you try it with regular
image viewing program it will try to unpack all pixels of the image in
the memory creating very large file and probably chocking.

Those fundamental issues are creating problems with software designed to
handle regular images (in memory) and there is nothing wrong with LOCI
or ImageJ.

That is why you really need to use special software for working with
Whole Slide Images , unless those images are small (under 1.2 GB *when
unpacked in memory* for 32bit architecture)

I hope it helps,

--
Vitali Khvatkov
Smart Imaging Technologies Co.
live.simagis.com



Serena Buscone wrote:

> Hi Curtis,
> thank you very much for your answer,  i tried to upload the images in omero
> but because i can't find find the svs file format in the list i can't
> upload them.
> I can change the file format in TIFF one but without compression each image
> become larger than 2 GB.
> Maby using the FTP server should be easier to upload svs files.
>
> Thanks for your collaboration
> Serena
>
>
>
> 2013/6/20 Curtis Rueden<[hidden email]>
>
>> Hi Serena,
>>
>> Thanks for the bug report.
>>
>> [CCing the ome-users list, which is the best place to discuss Bio-Formats
>> issues.]
>>
>>> Hi all, i work with fluorescence whole slide images obtained with an
>>> Aperio Scanner. I tried to open those svs files in imageJ and Fiji
>>> with LOCI plugin but it doesn't work. Some one can suggest me how to
>>> solve this problem ?
>> Could you please upload a sample non-working SVS file? It would help us
>> diagnose and fix the problem.
>>
>> If file is 500 MB or less, you can use:
>> http://qa.openmicroscopy.org.uk/qa/upload/
>>
>> Or if larger, let us know and we will send you FTP server credentials
>> off-list.
>>
>> Thanks,
>> Curtis
>>
>>
>> On Thu, Jun 20, 2013 at 4:58 AM, Serena Buscone<[hidden email]
>>> wrote:
>>> Hi all, i work with fluorescence whole slide images obtained with an
>>> Aperio Scanner. I tried to open those svs files in imageJ and Fiji with
>>> LOCI plugin but it doesn't work. Some one can suggest me how to solve
>> this
>>> problem ?
>>> Thank you very much
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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

[ctrueden]

Hi Vitali,

> Those fundamental issues are creating problems with software designed
> to handle regular images (in memory) and there is nothing wrong with
> LOCI or ImageJ.

I agree with everything you said about the challenges of working with whole
slide images.

However, I want to clarify that Bio-Formats specifically supports
extracting tiles of whatever size from many formats including
JPEG-compressed SVS. (Melissa Linkert actually put in a lot of research to
make that possible, since Java's built-in JPEG support cannot do that.) So
while ImageJ 1.x may not support *display* of extremely large image planes,
it is still possible to *process* them tile-by-tile using ImageJ.

Regards,
Curtis


On Fri, Jun 21, 2013 at 12:02 PM, Vitali Khvatkov <
[hidden email]> wrote:

> Perhaps the following information may help:
>
> Aperio SVS File is format with complex internal organization, it is
> created for Digital Pathology applications.
> It contains what is called tiled image pyramid, see illustration
> http://climserv.ipsl.**polytechnique.fr/**documentation/idl_help/images/**
> img_pyrm.gif<http://climserv.ipsl.polytechnique.fr/documentation/idl_help/images/img_pyrm.gif>
> This data structure is designed to enable fast viewing of the image *by
> special programs* , that can access just a portion of the image at a time,
> without loading whole image to computer memory.
>
> Yes, this structure is compatible with TIFF (BigTiff version) you even
> rename SVS to tiff and open it with TIFF viewer (if file is small that is)
> But  to access tiled pyramid correctly (without loading it to memory) you
> need special viewer.
>
> Compression is another problem: Your digital slide may be compressed with
> JPEG compression at 30:1 ratio , but if you try it with regular image
> viewing program it will try to unpack all pixels of the image in the memory
> creating very large file and probably chocking.
>
> Those fundamental issues are creating problems with software designed to
> handle regular images (in memory) and there is nothing wrong with LOCI or
> ImageJ.
>
> That is why you really need to use special software for working with Whole
> Slide Images , unless those images are small (under 1.2 GB *when unpacked
> in memory* for 32bit architecture)
>
> I hope it helps,
>
>
> --
> Vitali Khvatkov
> Smart Imaging Technologies Co.
> live.simagis.com
>
>
>
> Serena Buscone wrote:
>
>> Hi Curtis,
>> thank you very much for your answer,  i tried to upload the images in
>> omero
>> but because i can't find find the svs file format in the list i can't
>> upload them.
>> I can change the file format in TIFF one but without compression each
>> image
>> become larger than 2 GB.
>> Maby using the FTP server should be easier to upload svs files.
>>
>> Thanks for your collaboration
>> Serena
>>
>>
>>
>> 2013/6/20 Curtis Rueden<[hidden email]>
>>
>>  Hi Serena,
>>>
>>> Thanks for the bug report.
>>>
>>> [CCing the ome-users list, which is the best place to discuss Bio-Formats
>>> issues.]
>>>
>>>  Hi all, i work with fluorescence whole slide images obtained with an
>>>> Aperio Scanner. I tried to open those svs files in imageJ and Fiji
>>>> with LOCI plugin but it doesn't work. Some one can suggest me how to
>>>> solve this problem ?
>>>>
>>> Could you please upload a sample non-working SVS file? It would help us
>>> diagnose and fix the problem.
>>>
>>> If file is 500 MB or less, you can use:
>>> http://qa.openmicroscopy.org.**uk/qa/upload/<http://qa.openmicroscopy.org.uk/qa/upload/>
>>>
>>> Or if larger, let us know and we will send you FTP server credentials
>>> off-list.
>>>
>>> Thanks,
>>> Curtis
>>>
>>>
>>> On Thu, Jun 20, 2013 at 4:58 AM, Serena Buscone<serena.buscone@gmail.**
>>> com <[hidden email]>
>>>
>>>> wrote:
>>>> Hi all, i work with fluorescence whole slide images obtained with an
>>>> Aperio Scanner. I tried to open those svs files in imageJ and Fiji with
>>>> LOCI plugin but it doesn't work. Some one can suggest me how to solve
>>>>
>>> this
>>>
>>>> problem ?
>>>> Thank you very much
>>>>
>>>> --
>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>>>>
>>>>  --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>>>
>>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>

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

[ctrueden]

Hi Serena,

[CCing ome-users again.]

> Maby using the FTP server should be easier to upload svs files.

Yes, hopefully someone on the OMERO team can send you the login credentials
off-list (I don't have them).

Regards,
Curtis


On Fri, Jun 21, 2013 at 5:40 AM, Serena Buscone <[hidden email]>wrote:

> Hi Curtis,
> thank you very much for your answer,  i tried to upload the images in omero
> but because i can't find find the svs file format in the list i can't
> upload them.
> I can change the file format in TIFF one but without compression each image
> become larger than 2 GB.
> Maby using the FTP server should be easier to upload svs files.
>
> Thanks for your collaboration
> Serena
>
>
>
> 2013/6/20 Curtis Rueden <[hidden email]>
>
> > Hi Serena,
> >
> > Thanks for the bug report.
> >
> > [CCing the ome-users list, which is the best place to discuss Bio-Formats
> > issues.]
> >
> > > Hi all, i work with fluorescence whole slide images obtained with an
> > > Aperio Scanner. I tried to open those svs files in imageJ and Fiji
> > > with LOCI plugin but it doesn't work. Some one can suggest me how to
> > > solve this problem ?
> >
> > Could you please upload a sample non-working SVS file? It would help us
> > diagnose and fix the problem.
> >
> > If file is 500 MB or less, you can use:
> > http://qa.openmicroscopy.org.uk/qa/upload/
> >
> > Or if larger, let us know and we will send you FTP server credentials
> > off-list.
> >
> > Thanks,
> > Curtis
> >
> >
> > On Thu, Jun 20, 2013 at 4:58 AM, Serena Buscone <
> [hidden email]
> > >wrote:
> >
> > > Hi all, i work with fluorescence whole slide images obtained with an
> > > Aperio Scanner. I tried to open those svs files in imageJ and Fiji with
> > > LOCI plugin but it doesn't work. Some one can suggest me how to solve
> > this
> > > problem ?
> > > Thank you very much
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Serena Buscone]

Hi Curtis,

can you suggest me a mail adress to contact someone on the OMERO team or I
can simply leave a message on the community forum?

Thanks for your help
Serena


2013/6/22 Curtis Rueden <[hidden email]>

> Hi Serena,
>
> [CCing ome-users again.]
>
> > Maby using the FTP server should be easier to upload svs files.
>
> Yes, hopefully someone on the OMERO team can send you the login credentials
> off-list (I don't have them).
>
> Regards,
> Curtis
>
>
> On Fri, Jun 21, 2013 at 5:40 AM, Serena Buscone <[hidden email]
> >wrote:
>
> > Hi Curtis,
> > thank you very much for your answer,  i tried to upload the images in
> omero
> > but because i can't find find the svs file format in the list i can't
> > upload them.
> > I can change the file format in TIFF one but without compression each
> image
> > become larger than 2 GB.
> > Maby using the FTP server should be easier to upload svs files.
> >
> > Thanks for your collaboration
> > Serena
> >
> >
> >
> > 2013/6/20 Curtis Rueden <[hidden email]>
> >
> > > Hi Serena,
> > >
> > > Thanks for the bug report.
> > >
> > > [CCing the ome-users list, which is the best place to discuss
> Bio-Formats
> > > issues.]
> > >
> > > > Hi all, i work with fluorescence whole slide images obtained with an
> > > > Aperio Scanner. I tried to open those svs files in imageJ and Fiji
> > > > with LOCI plugin but it doesn't work. Some one can suggest me how to
> > > > solve this problem ?
> > >
> > > Could you please upload a sample non-working SVS file? It would help us
> > > diagnose and fix the problem.
> > >
> > > If file is 500 MB or less, you can use:
> > > http://qa.openmicroscopy.org.uk/qa/upload/
> > >
> > > Or if larger, let us know and we will send you FTP server credentials
> > > off-list.
> > >
> > > Thanks,
> > > Curtis
> > >
> > >
> > > On Thu, Jun 20, 2013 at 4:58 AM, Serena Buscone <
> > [hidden email]
> > > >wrote:
> > >
> > > > Hi all, i work with fluorescence whole slide images obtained with an
> > > > Aperio Scanner. I tried to open those svs files in imageJ and Fiji
> with
> > > > LOCI plugin but it doesn't work. Some one can suggest me how to solve
> > > this
> > > > problem ?
> > > > Thank you very much
> > > >
> > > > --
> > > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > > >
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Kevin W Eliceiri]

Hi Serena,

We handle all Bio-Formats support on our Open Microscopy Environment users forum, see http://www.openmicroscopy.org/site/community/mailing-lists for details. This is the OME Users list that Curtis cced. If you post there a member of our team will help you.

best,
kevin

On 06/26/13, Serena Buscone  wrote:

> Hi Curtis,
>
> can you suggest me a mail adress to contact someone on the OMERO team or I
> can simply leave a message on the community forum?
>
> Thanks for your help
> Serena
>
>
> 2013/6/22 Curtis Rueden <[hidden email]>
>
> > Hi Serena,
> >
> > [CCing ome-users again.]
> >
> > > Maby using the FTP server should be easier to upload svs files.
> >
> > Yes, hopefully someone on the OMERO team can send you the login credentials
> > off-list (I don't have them).
> >
> > Regards,
> > Curtis
> >
> >
> > On Fri, Jun 21, 2013 at 5:40 AM, Serena Buscone <[hidden email]
> > >wrote:
> >
> > > Hi Curtis,
> > > thank you very much for your answer, i tried to upload the images in
> > omero
> > > but because i can't find find the svs file format in the list i can't
> > > upload them.
> > > I can change the file format in TIFF one but without compression each
> > image
> > > become larger than 2 GB.
> > > Maby using the FTP server should be easier to upload svs files.
> > >
> > > Thanks for your collaboration
> > > Serena
> > >
> > >
> > >
> > > 2013/6/20 Curtis Rueden <[hidden email]>
> > >
> > > > Hi Serena,
> > > >
> > > > Thanks for the bug report.
> > > >
> > > > [CCing the ome-users list, which is the best place to discuss
> > Bio-Formats
> > > > issues.]
> > > >
> > > > > Hi all, i work with fluorescence whole slide images obtained with an
> > > > > Aperio Scanner. I tried to open those svs files in imageJ and Fiji
> > > > > with LOCI plugin but it doesn't work. Some one can suggest me how to
> > > > > solve this problem ?
> > > >
> > > > Could you please upload a sample non-working SVS file? It would help us
> > > > diagnose and fix the problem.
> > > >
> > > > If file is 500 MB or less, you can use:
> > > > http://qa.openmicroscopy.org.uk/qa/upload/
> > > >
> > > > Or if larger, let us know and we will send you FTP server credentials
> > > > off-list.
> > > >
> > > > Thanks,
> > > > Curtis
> > > >
> > > >
> > > > On Thu, Jun 20, 2013 at 4:58 AM, Serena Buscone <
> > > [hidden email]
> > > > >wrote:
> > > >
> > > > > Hi all, i work with fluorescence whole slide images obtained with an
> > > > > Aperio Scanner. I tried to open those svs files in imageJ and Fiji
> > with
> > > > > LOCI plugin but it doesn't work. Some one can suggest me how to solve
> > > > this
> > > > > problem ?
> > > > > Thank you very much
> > > > >
> >

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[Vitali Khvatkov-2]

Yes, it is certainly possible to through the entire image extracting
tiles one by one, but let me illustrate the difference - in the end one
picture is worth a thousand words, right? :)

Here is live example showing work of software designed to handle SVS
image pyramid in its entirety for viewing  and processing of such
images: http://goo.gl/TLYB5

As you pan, zoom and switch analysis overlays, you can see see
"instant"  access to the image - "on the fly". The image was not
previously re-tiled, so if you upload new svs file it will be viewable
instantly (with correct scale, since pixel size is a part of SVS format
and software knows about it)

This is possible because the software is designed to use all layers of
the image pyramid, together, to process this complex structure, and this
makes a lot of difference in practical application, such as viewing or
processing of a Whole Slide Image.

Regards,

--
Vitali Khvatkov
Smart Imaging Technologies Co.
live.simagis.com



Curtis Rueden wrote:

> Hi Vitali,
>
>> Those fundamental issues are creating problems with software designed
>> to handle regular images (in memory) and there is nothing wrong with
>> LOCI or ImageJ.
>
> I agree with everything you said about the challenges of working with whole
> slide images.
>
> However, I want to clarify that Bio-Formats specifically supports
> extracting tiles of whatever size from many formats including
> JPEG-compressed SVS. (Melissa Linkert actually put in a lot of research to
> make that possible, since Java's built-in JPEG support cannot do that.) So
> while ImageJ 1.x may not support *display* of extremely large image planes,
> it is still possible to *process* them tile-by-tile using ImageJ.
>
> Regards,
> Curtis
>
>
> On Fri, Jun 21, 2013 at 12:02 PM, Vitali Khvatkov<
> [hidden email]>  wrote:
>
>> Perhaps the following information may help:
>>
>> Aperio SVS File is format with complex internal organization, it is
>> created for Digital Pathology applications.
>> It contains what is called tiled image pyramid, see illustration
>> http://climserv.ipsl.**polytechnique.fr/**documentation/idl_help/images/**
>> img_pyrm.gif<http://climserv.ipsl.polytechnique.fr/documentation/idl_help/images/img_pyrm.gif>
>> This data structure is designed to enable fast viewing of the image *by
>> special programs* , that can access just a portion of the image at a time,
>> without loading whole image to computer memory.
>>
>> Yes, this structure is compatible with TIFF (BigTiff version) you even
>> rename SVS to tiff and open it with TIFF viewer (if file is small that is)
>> But  to access tiled pyramid correctly (without loading it to memory) you
>> need special viewer.
>>
>> Compression is another problem: Your digital slide may be compressed with
>> JPEG compression at 30:1 ratio , but if you try it with regular image
>> viewing program it will try to unpack all pixels of the image in the memory
>> creating very large file and probably chocking.
>>
>> Those fundamental issues are creating problems with software designed to
>> handle regular images (in memory) and there is nothing wrong with LOCI or
>> ImageJ.
>>
>> That is why you really need to use special software for working with Whole
>> Slide Images , unless those images are small (under 1.2 GB *when unpacked
>> in memory* for 32bit architecture)
>>
>> I hope it helps,
>>
>>
>> --
>> Vitali Khvatkov
>> Smart Imaging Technologies Co.
>> live.simagis.com
>>
>>
>>
>> Serena Buscone wrote:
>>
>>> Hi Curtis,
>>> thank you very much for your answer,  i tried to upload the images in
>>> omero
>>> but because i can't find find the svs file format in the list i can't
>>> upload them.
>>> I can change the file format in TIFF one but without compression each
>>> image
>>> become larger than 2 GB.
>>> Maby using the FTP server should be easier to upload svs files.
>>>
>>> Thanks for your collaboration
>>> Serena
>>>
>>>
>>>
>>> 2013/6/20 Curtis Rueden<[hidden email]>
>>>
>>>   Hi Serena,
>>>> Thanks for the bug report.
>>>>
>>>> [CCing the ome-users list, which is the best place to discuss Bio-Formats
>>>> issues.]
>>>>
>>>>   Hi all, i work with fluorescence whole slide images obtained with an
>>>>> Aperio Scanner. I tried to open those svs files in imageJ and Fiji
>>>>> with LOCI plugin but it doesn't work. Some one can suggest me how to
>>>>> solve this problem ?
>>>>>
>>>> Could you please upload a sample non-working SVS file? It would help us
>>>> diagnose and fix the problem.
>>>>
>>>> If file is 500 MB or less, you can use:
>>>> http://qa.openmicroscopy.org.**uk/qa/upload/<http://qa.openmicroscopy.org.uk/qa/upload/>
>>>>
>>>> Or if larger, let us know and we will send you FTP server credentials
>>>> off-list.
>>>>
>>>> Thanks,
>>>> Curtis
>>>>
>>>>
>>>> On Thu, Jun 20, 2013 at 4:58 AM, Serena Buscone<serena.buscone@gmail.**
>>>> com<[hidden email]>
>>>>
>>>>> wrote:
>>>>> Hi all, i work with fluorescence whole slide images obtained with an
>>>>> Aperio Scanner. I tried to open those svs files in imageJ and Fiji with
>>>>> LOCI plugin but it doesn't work. Some one can suggest me how to solve
>>>>>
>>>> this
>>>>
>>>>> problem ?
>>>>> Thank you very much
>>>>>
>>>>> --
>>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>>>>>
>>>>>   --
>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>>>>
>>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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

[Jason Swedlow-2]

Hi All-

Just to reiterate the statements from Curtis and Kevin regarding OME's open
source resources for slide images;

-- Bio-Formats (http://www.openmicroscopy.org/site/products/bio-formats) is
a Java library that provides access >130 proprietary image file formats,
and with regard to this thread, multiple virtual slide formats (e.g., .svs,
.afi. ndpi, .scn).  Curtis highlighted the work Melissa Linkert, the lead
Bio-Formats developer, has done to optimize Bio-Formats for this purpose.
This includes reading the image data natively from the formats.

-- OMERO (http://www.openmicroscopy.org/site/products/omero) is a
client-server data management application that, through Bio-Formats,
supports these virtual slide formats, and can be used for other large
images as well.  One example is at the JCB
DataViewer<http://jcb-dataviewer.rupress.org>,
and shows a 5 day old zebrafish
embryo<http://v.jcb-dataviewer.glencoesoftware.com/webclient/img_detail/201/>recorded
at EM resolution by Ray Ravelli and colleagues.

All OME software and documentation are available at
http://openmicroscopy.org.

As Kevin noted, open, public discussions are at
http://www.openmicroscopy.org/community/.

Of course, Albert Cardona and colleagues have developed and continue to
drive CATMAID (http://catmaid.org/), another widely used open source tool
for viewing large images.

Cheers,

Jason


On Thu, Jun 27, 2013 at 6:47 PM, Vitali Khvatkov <[hidden email]
> wrote:

> Yes, it is certainly possible to through the entire image extracting tiles
> one by one, but let me illustrate the difference - in the end one picture
> is worth a thousand words, right? :)
>
> Here is live example showing work of software designed to handle SVS image
> pyramid in its entirety for viewing  and processing of such images:
> http://goo.gl/TLYB5
>
> As you pan, zoom and switch analysis overlays, you can see see "instant"
>  access to the image - "on the fly". The image was not previously re-tiled,
> so if you upload new svs file it will be viewable instantly (with correct
> scale, since pixel size is a part of SVS format and software knows about it)
>
> This is possible because the software is designed to use all layers of the
> image pyramid, together, to process this complex structure, and this makes
> a lot of difference in practical application, such as viewing or processing
> of a Whole Slide Image.
>
> Regards,
>
>
> --
> Vitali Khvatkov
> Smart Imaging Technologies Co.
> live.simagis.com
>
>
>
> Curtis Rueden wrote:
>
>> Hi Vitali,
>>
>>  Those fundamental issues are creating problems with software designed
>>> to handle regular images (in memory) and there is nothing wrong with
>>> LOCI or ImageJ.
>>>
>>
>> I agree with everything you said about the challenges of working with
>> whole
>> slide images.
>>
>> However, I want to clarify that Bio-Formats specifically supports
>> extracting tiles of whatever size from many formats including
>> JPEG-compressed SVS. (Melissa Linkert actually put in a lot of research to
>> make that possible, since Java's built-in JPEG support cannot do that.) So
>> while ImageJ 1.x may not support *display* of extremely large image
>> planes,
>> it is still possible to *process* them tile-by-tile using ImageJ.
>>
>> Regards,
>> Curtis
>>
>>
>> On Fri, Jun 21, 2013 at 12:02 PM, Vitali Khvatkov<
>> [hidden email]>  wrote:
>>
>>  Perhaps the following information may help:
>>>
>>> Aperio SVS File is format with complex internal organization, it is
>>> created for Digital Pathology applications.
>>> It contains what is called tiled image pyramid, see illustration
>>> http://climserv.ipsl.**polytec**hnique.fr/**documentation/idl_**
>>> help/images/**<http://polytechnique.fr/**documentation/idl_help/images/**>
>>> img_pyrm.gif<http://climserv.**ipsl.polytechnique.fr/**
>>> documentation/idl_help/images/**img_pyrm.gif<http://climserv.ipsl.polytechnique.fr/documentation/idl_help/images/img_pyrm.gif>
>>> >
>>> This data structure is designed to enable fast viewing of the image *by
>>> special programs* , that can access just a portion of the image at a
>>> time,
>>> without loading whole image to computer memory.
>>>
>>> Yes, this structure is compatible with TIFF (BigTiff version) you even
>>> rename SVS to tiff and open it with TIFF viewer (if file is small that
>>> is)
>>> But  to access tiled pyramid correctly (without loading it to memory) you
>>> need special viewer.
>>>
>>> Compression is another problem: Your digital slide may be compressed with
>>> JPEG compression at 30:1 ratio , but if you try it with regular image
>>> viewing program it will try to unpack all pixels of the image in the
>>> memory
>>> creating very large file and probably chocking.
>>>
>>> Those fundamental issues are creating problems with software designed to
>>> handle regular images (in memory) and there is nothing wrong with LOCI or
>>> ImageJ.
>>>
>>> That is why you really need to use special software for working with
>>> Whole
>>> Slide Images , unless those images are small (under 1.2 GB *when unpacked
>>> in memory* for 32bit architecture)
>>>
>>> I hope it helps,
>>>
>>>
>>> --
>>> Vitali Khvatkov
>>> Smart Imaging Technologies Co.
>>> live.simagis.com
>>>
>>>
>>>
>>> Serena Buscone wrote:
>>>
>>>  Hi Curtis,
>>>> thank you very much for your answer,  i tried to upload the images in
>>>> omero
>>>> but because i can't find find the svs file format in the list i can't
>>>> upload them.
>>>> I can change the file format in TIFF one but without compression each
>>>> image
>>>> become larger than 2 GB.
>>>> Maby using the FTP server should be easier to upload svs files.
>>>>
>>>> Thanks for your collaboration
>>>> Serena
>>>>
>>>>
>>>>
>>>> 2013/6/20 Curtis Rueden<[hidden email]>
>>>>
>>>>   Hi Serena,
>>>>
>>>>> Thanks for the bug report.
>>>>>
>>>>> [CCing the ome-users list, which is the best place to discuss
>>>>> Bio-Formats
>>>>> issues.]
>>>>>
>>>>>   Hi all, i work with fluorescence whole slide images obtained with an
>>>>>
>>>>>> Aperio Scanner. I tried to open those svs files in imageJ and Fiji
>>>>>> with LOCI plugin but it doesn't work. Some one can suggest me how to
>>>>>> solve this problem ?
>>>>>>
>>>>>>  Could you please upload a sample non-working SVS file? It would help
>>>>> us
>>>>> diagnose and fix the problem.
>>>>>
>>>>> If file is 500 MB or less, you can use:
>>>>> http://qa.openmicroscopy.org.****uk/qa/upload/<http://qa.**
>>>>> openmicroscopy.org.uk/qa/**upload/<http://qa.openmicroscopy.org.uk/qa/upload/>
>>>>> >
>>>>>
>>>>> Or if larger, let us know and we will send you FTP server credentials
>>>>> off-list.
>>>>>
>>>>> Thanks,
>>>>> Curtis
>>>>>
>>>>>
>>>>> On Thu, Jun 20, 2013 at 4:58 AM, Serena Buscone<serena.buscone@gmail.*
>>>>> ***
>>>>> com<[hidden email]>
>>>>>
>>>>>  wrote:
>>>>>> Hi all, i work with fluorescence whole slide images obtained with an
>>>>>> Aperio Scanner. I tried to open those svs files in imageJ and Fiji
>>>>>> with
>>>>>> LOCI plugin but it doesn't work. Some one can suggest me how to solve
>>>>>>
>>>>>>  this
>>>>>
>>>>>  problem ?
>>>>>> Thank you very much
>>>>>>
>>>>>> --
>>>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.****html<http://imagej.nih.gov/ij/list.**html>
>>>>>> <http://imagej.nih.gov/**ij/list.html<http://imagej.nih.gov/ij/list.html>
>>>>>> >
>>>>>>
>>>>>>   --
>>>>>>
>>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.****html<http://imagej.nih.gov/ij/list.**html>
>>>>> <http://imagej.nih.gov/**ij/list.html<http://imagej.nih.gov/ij/list.html>
>>>>> >
>>>>>
>>>>>
>>>>>  --
>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.****html<http://imagej.nih.gov/ij/list.**html>
>>>> <http://imagej.nih.gov/**ij/list.html<http://imagej.nih.gov/ij/list.html>
>>>> >
>>>>
>>>>  --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.****html<http://imagej.nih.gov/ij/list.**html>
>>> <http://imagej.nih.gov/**ij/list.html<http://imagej.nih.gov/ij/list.html>
>>> >
>>>
>>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>>
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>

--
**************************
Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
MSI/WTB/JBC Complex
University of Dundee
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phone [phone]
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