[ome-users] Calling API to import Aperio.svs Digital Slide

[Curtis Rueden]

Hi Mark,


> I can not get bfconvert to work directly, get a constant
> "c:\program files\imagej" not expected.
> My syntax is:
> from prompt at c:\program files\imagej:
> bfconvert Slide1.svs slide1.jpg


I don't know what scripting language that is, but did you try putting
"C:\program files\imagej" in double quotes? Your path contains a space and
you need to either escape spaces or quote the whole relevant string.


> I also need to pass in crop parameters.


Run "bfconvert" with no arguments to get a list of available command line
parameters, which includes cropping.

Regards,
Curtis


On Mon, Jul 30, 2012 at 11:04 AM, <mark.plaskow at americanhealthtechnology.com
> wrote:

> Curtis,
>
> Thanks a lot for the prompt reply. The BioFormats tool is excellent and
> all of you are worth a great deal with your technical skills in the
> market.
>
> I can not get bfconvert to work directly, get a constant "c:\program
> files\imagej" not expected.
>
> My syntax is:
>
> from prompt at c:\program files\imagej:
>
> bfconvert Slide1.svs slide1.jpg
>
> I also need to pass in crop parameters.
>
> Thanks a lot!
>
>
>
> > -------- Original Message --------
> > Subject: Re: [ome-users] Calling API to import Aperio.svs Digital Slide
> > From: Curtis Rueden <ctrueden at wisc.edu>
> > Date: Mon, July 30, 2012 11:58 am
> > To: mark.plaskow at americanhealthtechnology.com
> > Cc: ome-users at lists.openmicroscopy.org.uk
> >
> > Hi Mark,
> >
> >
> > With a .NET application, what is the simplest way to call an API for
> >
> >
> > importing an Aperio.svs digital slide, along with being able to save
> > it's metadata?
>
> >
> > The simplest way is to make a system call to one of the Bio-Formats
> command line tools (http://loci.wisc.edu/bio-formats/command-line-tools).
> For example, you could call "bfconvert" to convert it to a temporary file
> in a format your application understands, then open that temporary file
> normally from .NET.
> >
> >
> >
> >
> > The next-most-simple (and more performant) would be to write some Java
> code that uses Bio-Formats to do exactly what you want, and then use a
> system call with pipes to pass the inputs, and receive the outputs, within
> your .NET application.
> >
> >
> >
> >
> > The most powerful and flexible way would be to use the Bio-Formats C++
> bindings (http://loci.wisc.edu/bio-formats/bio-formats-c-bindings) to
> access Bio-Formats via JNI in-process. Then you would have full access to
> the entire Bio-Formats API, but with more dependencies (need to link to
> Boost Thread library as well as Java's JVM.DLL).
>
> >
> >
> >
> >
> > For more details, see this page:
> >     http://loci.wisc.edu/bio-formats/interfacing-non-java-code
> >
> >
> >
> > Regards,
> > Curtis
> >
> > On Mon, Jul 30, 2012 at 10:45 AM, <
> mark.plaskow at americanhealthtechnology.com> wrote:
> >
> >
> > With a .NET application, what is the simplest way to call an API for
> > importing an Aperio.svs digital slide, along with being able to save
> > it's metadata?
>
> >
> >
> >
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >
> >
> >
>
>
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