<div>Hi Mark,</div><div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><br></blockquote><div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
I can not get bfconvert to work directly, get a constant "c:\program files\imagej" not expected.<br>My syntax is:<br>from prompt at c:\program files\imagej:<br>bfconvert Slide1.svs slide1.jpg</blockquote><div><br>
</div><div>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.</div>
<div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><br></blockquote><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
I also need to pass in crop parameters.</blockquote></div><div><br></div><div>Run "bfconvert" with no arguments to get a list of available command line parameters, which includes cropping.</div><div><br></div><div>
Regards,</div><div>Curtis</div><div><br><br><div class="gmail_quote">On Mon, Jul 30, 2012 at 11:04 AM, <span dir="ltr"><<a href="mailto:mark.plaskow@americanhealthtechnology.com" target="_blank">mark.plaskow@americanhealthtechnology.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Curtis,<br>
<br>
Thanks a lot for the prompt reply. The BioFormats tool is excellent and<br>
all of you are worth a great deal with your technical skills in the<br>
market.<br>
<br>
I can not get bfconvert to work directly, get a constant "c:\program<br>
files\imagej" not expected.<br>
<br>
My syntax is:<br>
<br>
from prompt at c:\program files\imagej:<br>
<br>
bfconvert Slide1.svs slide1.jpg<br>
<br>
I also need to pass in crop parameters.<br>
<br>
Thanks a lot!<div class="im"><br>
<br>
<br>
> -------- Original Message --------<br>
> Subject: Re: [ome-users] Calling API to import Aperio.svs Digital Slide<br>
> From: Curtis Rueden <<a href="mailto:ctrueden@wisc.edu" target="_blank">ctrueden@wisc.edu</a>><br>
> Date: Mon, July 30, 2012 11:58 am<br>
> To: <a href="mailto:mark.plaskow@americanhealthtechnology.com" target="_blank">mark.plaskow@americanhealthtechnology.com</a><br>
> Cc: <a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a><br>
> <br>
> Hi Mark,<br>
> <br>
> <br>
> With a .NET application, what is the simplest way to call an API for<br>
> <br>
> <br>
> importing an Aperio.svs digital slide, along with being able to save<br></div>
> it's metadata?<div class="im"><br>
> <br>
> The simplest way is to make a system call to one of the Bio-Formats command line tools (<a href="http://loci.wisc.edu/bio-formats/command-line-tools" target="_blank">http://loci.wisc.edu/bio-formats/command-line-tools</a>). 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.<br>
> <br>
> <br>
> <br>
> <br>
> 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.<br>
> <br>
> <br>
> <br>
> <br></div>
> The most powerful and flexible way would be to use the Bio-Formats C++ bindings (<a href="http://loci.wisc.edu/bio-formats/bio-formats-c-bindings" target="_blank">http://loci.wisc.edu/bio-formats/bio-formats-c-bindings</a>) 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).<div class="im">
<br>
> <br>
> <br>
> <br>
> <br>
> For more details, see this page:<br>
> <a href="http://loci.wisc.edu/bio-formats/interfacing-non-java-code" target="_blank">http://loci.wisc.edu/bio-formats/interfacing-non-java-code</a><br>
> <br>
> <br>
> <br>
> Regards,<br>
> Curtis<br>
> <br>
> On Mon, Jul 30, 2012 at 10:45 AM, <<a href="mailto:mark.plaskow@americanhealthtechnology.com" target="_blank">mark.plaskow@americanhealthtechnology.com</a>> wrote:<br>
> <br>
> <br>
> With a .NET application, what is the simplest way to call an API for<br>
> importing an Aperio.svs digital slide, along with being able to save<br></div>
> it's metadata?<div class="HOEnZb"><div class="h5"><br>
> <br>
> <br>
> <br>
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> <br>
> <br>
> <br>
<br>
</div></div></blockquote></div><br></div>