Olympus .vsi file format?

[Kenneth Sloan-2]

Does anyone have a plug-in to read/write Olympus .vsi files?

Or...documentation sufficient for *me* to write one?

--
Kenneth Sloan
[hidden email]

[Daniel James White]

Dear Kenneth,


If  you are going write a reader for these .vsi,
I strongly suggest you do it in close collaboration with the bio-formats team from LOCI,

you can checkout the bio-formats code via svn,
and talk to those guys about how to write a new reader,
and reuse all the parts from bio-formats possible.

Then you can contribute the reader to the bio-formats project,
and help out al the others who have these files.

Maybe my local Olympus rep (ccd here)
can provide us with the file specification documents
or at least point us to where to find them.

I never heard of this file format before.

What  olympus imaging system is it from ?

cheers
Dan


On Sep 27, 2010, at 6:00 AM, IMAGEJ automatic digest system wrote:

> Date:    Sat, 25 Sep 2010 23:03:55 -0500
> From:    Kenneth Sloan <[hidden email]>
> Subject: Olympus .vsi file format?
>
> Does anyone have a plug-in to read/write Olympus .vsi files?
>
> Or...documentation sufficient for *me* to write one?
>
> --
> Kenneth Sloan
> [hidden email]

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

[phone] (German Mobile)
[phone] (Work phone at MPI-CBG)
[phone] (Fax MPI-CBG LMF)

http://www.bioimagexd.net  BioImageXD
http://pacific.mpi-cbg.de                Fiji -  is just ImageJ (Batteries Included)
http://www.chalkie.org.uk                Dan's Homepages
https://ifn.mpi-cbg.de  Dresden Imaging Facility Network
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )

[Gabriel Landini]

On Monday 27 Sep 2010  10:47:58 Daniel James White wrote:

> I never heard of this file format before.
> What  olympus imaging system is it from ?

Hi
It is the 'virtual slide' format used in the Olympus slide scanners (dotSlide
and other models).

I have the suspicion (but hope not) that this might be a closed format.
If you have the Olympus scanner system accessible, then one should be able to
re-save the data in tif tiles (non-lossy) or jpeg (lossy).

Cheers

Gabriel

[Kenneth Sloan]

I also suspect that it's a closed format - I was hoping that someone would disabuse me of that idea.
Right now, I'm one person removed from the local Olympus rep, so I haven't had a chance to ask the
right questions.  The impression I get from various literature
is that the format might be closed - but sometimes it's possible to get documentation if you ask nicely.
Sometimes, if you ask 17 times, they actually write the documentation...

I've found a couple of systems that claim to read VSI files (anyone heard of mScope?)

The system does indeed export all sorts of formats which I can deal with - but (warning: I have not
actually touched the system, yet) a colleague reports that the TIFF files he's getting are not as good
as the VSI files displayed using their software.  I'm hoping that he simply hasn't read the entire manual, yet.

If we can import and export, I can build a workaround - but I have a strong preference for getting
the RAW data out of any instrument ASAP and processing it with code that I have written.   Sometimes "lossless" is
too lossy.

Ah...here's the spec sheet - we are talking about the cellSens imaging software.  Spec sheet says it can read and write:
VSI, JPEG, JPEG2000, TIFF, BMP, AVI, PNG.  Read-only: GIFF, PSD, TIFF (DP-BSW, FSX100,MetaMorph), OIR/OIB(Fluoview format)...

I understand that we have actually managed to get the software to give us a PSD file.  Hmmm...I guess that's what they mean by "read-only".  These images are excellent, and we're using Photoshop to convert to beautiful TIFF.  I'm told that the TIFF files created directly are deficient (low resolution?  not deep enough?  don't know).

So...cellSens->PSD->Photoshop->TIFF appears to work.  

cellSens->TIFF *should* work - but something is not understood at the moment.

I would *like* to directly read the VSI files - but I suspect that will be more trouble than it will be worth.

My collaborator would dearly love to IMPORT a PSD file (after marking up the image using Photoshop).  I doubt that will
be possible.

We don't want to build a commercial product, and we are purchasing the software.  Is is too much to ask for documentation of
the file formats created by the software?

Closed formats are the bane of my existence!  Reverse-engineering them is a royal PITA.

Oh well...I tried.


On another topic: will there be anyone in Luxembourg interested in OCT imaging/segmentation?  If so, an informal lunch or dinner "session" might be interesting.


On Sep 27, 2010, at 04:54 , Gabriel Landini wrote:

> On Monday 27 Sep 2010  10:47:58 Daniel James White wrote:
>
>> I never heard of this file format before.
>> What  olympus imaging system is it from ?
>
> Hi
> It is the 'virtual slide' format used in the Olympus slide scanners (dotSlide
> and other models).
>
> I have the suspicion (but hope not) that this might be a closed format.
> If you have the Olympus scanner system accessible, then one should be able to
> re-save the data in tif tiles (non-lossy) or jpeg (lossy).
>
> Cheers
>
> Gabriel

--
Kenneth Sloan
[hidden email]

[Melissa Linkert-2]

Hi Kenneth,

As Dan mentioned, support for the VSI files can definitely be added to
Bio-Formats (http://loci.wisc.edu/bio-formats).  However, you do not
need to do this work yourself - if you can provide us (the Bio-Formats
developers) with a few example VSI files, we will happily work toward
adding support for these files in the near future.  I will send you our SFTP
server details off-list, in case you are interested in sending a few
files.

It would, of course, be wonderful to have a specification or some other
documentation, but for the majority of file formats that we have seen
this kind of information is simply not available.

Regards,
-Melissa

On Mon, Sep 27, 2010 at 09:36:59PM -0500, Kenneth Sloan wrote:

> I also suspect that it's a closed format - I was hoping that someone would disabuse me of that idea.
> Right now, I'm one person removed from the local Olympus rep, so I haven't had a chance to ask the
> right questions.  The impression I get from various literature
> is that the format might be closed - but sometimes it's possible to get documentation if you ask nicely.
> Sometimes, if you ask 17 times, they actually write the documentation...
>
> I've found a couple of systems that claim to read VSI files (anyone heard of mScope?)
>
> The system does indeed export all sorts of formats which I can deal with - but (warning: I have not
> actually touched the system, yet) a colleague reports that the TIFF files he's getting are not as good
> as the VSI files displayed using their software.  I'm hoping that he simply hasn't read the entire manual, yet.
>
> If we can import and export, I can build a workaround - but I have a strong preference for getting
> the RAW data out of any instrument ASAP and processing it with code that I have written.   Sometimes "lossless" is
> too lossy.
>
> Ah...here's the spec sheet - we are talking about the cellSens imaging software.  Spec sheet says it can read and write:
> VSI, JPEG, JPEG2000, TIFF, BMP, AVI, PNG.  Read-only: GIFF, PSD, TIFF (DP-BSW, FSX100,MetaMorph), OIR/OIB(Fluoview format)...
>
> I understand that we have actually managed to get the software to give us a PSD file.  Hmmm...I guess that's what they mean by "read-only".  These images are excellent, and we're using Photoshop to convert to beautiful TIFF.  I'm told that the TIFF files created directly are deficient (low resolution?  not deep enough?  don't know).
>
> So...cellSens->PSD->Photoshop->TIFF appears to work.  
>
> cellSens->TIFF *should* work - but something is not understood at the moment.
>
> I would *like* to directly read the VSI files - but I suspect that will be more trouble than it will be worth.
>
> My collaborator would dearly love to IMPORT a PSD file (after marking up the image using Photoshop).  I doubt that will
> be possible.
>
> We don't want to build a commercial product, and we are purchasing the software.  Is is too much to ask for documentation of
> the file formats created by the software?
>
> Closed formats are the bane of my existence!  Reverse-engineering them is a royal PITA.
>
> Oh well...I tried.
>
>
> On another topic: will there be anyone in Luxembourg interested in OCT imaging/segmentation?  If so, an informal lunch or dinner "session" might be interesting.
>
>
> On Sep 27, 2010, at 04:54 , Gabriel Landini wrote:
>
> > On Monday 27 Sep 2010  10:47:58 Daniel James White wrote:
> >
> >> I never heard of this file format before.
> >> What  olympus imaging system is it from ?
> >
> > Hi
> > It is the 'virtual slide' format used in the Olympus slide scanners (dotSlide
> > and other models).
> >
> > I have the suspicion (but hope not) that this might be a closed format.
> > If you have the Olympus scanner system accessible, then one should be able to
> > re-save the data in tif tiles (non-lossy) or jpeg (lossy).
> >
> > Cheers
> >
> > Gabriel
>
> --
> Kenneth Sloan
> [hidden email]