Hi Mark,<br><br>Thank you for the email and invaluable help. The bioformats-itk plugin is wonderful. I am attaching my script here to help you debug. Let me know if you have any questions on my script. I am starting with a 5D (XYZTC) image and trying to write out all the 3D timepoints for the first channel.<br>
<br>Kishore<br><br><div class="gmail_quote">On Fri, Oct 12, 2012 at 12:19 PM, Mark Hiner <span dir="ltr"><<a href="mailto:hinerm@gmail.com" target="_blank">hinerm@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Kishore,<br><br> I helped develop the bf-itk-pipe plugin and am investigating your issue right now. <br><br> What you're doing seems reasonable, so I'm trying to determine if there's a bug in the plugin. My goal is to have some working example code for you (and a fix if necessary) by the end of the day.<br>
<br>Thank you for using our plugin! I hope we can get it working for you soon.<br><br>- Mark<br><br><div class="gmail_quote"><div><div class="h5">On Fri, Oct 12, 2012 at 10:54 AM, Kishore Mosaliganti <span dir="ltr"><<a href="mailto:kishoreraom@gmail.com" target="_blank">kishoreraom@gmail.com</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">Dear ITK and OME users,<br><br>To further elaborate, I figured that this has nothing to do with the itkStreamingImageFilter.<br>
<br>Instead, the itkImageFileReader seems to be extracting the same image region although I update the requested region in the BioformatsImageIO class :;<br>
<br> itk::BioFormatsImageIO::Pointer io = itk::BioFormatsImageIO::New();<br> io->SetIORegion( region ); // doesn't make a difference in terms of image data extracted. Its always from the beginning.<br><br> ReaderType::Pointer reader = ReaderType::New();<br>
reader->SetFileName(argv[1]);<br> reader->SetImageIO(io);<br> reader->Update();<br><br>So, my general question is whether the BioformatsImageIO expects the whole LSM image to be loaded into memory before writing it out? I would like to specify small image regions since my LSM is too large to be fully loaded into memory. How else can I stream data from large LSM?<br>
<br>Thanks,<br><br>Kishore<br><br><br><div class="gmail_quote">On Fri, Oct 12, 2012 at 8:53 AM, Kishore Mosaliganti <span dir="ltr"><<a href="mailto:kishoreraom@gmail.com" target="_blank">kishoreraom@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi all,<br><br>I am trying to use bioformats and itk. I downloaded
and compiled bf-itk-pipe using cmake by linking against ITK 3.2:<br><br><a href="https://github.com/openmicroscopy/bioformats/tree/develop/components/native/bf-itk-pipe" target="_blank">https://github.com/openmicroscopy/bioformats/tree/develop/components/native/bf-itk-pipe</a><br>
<br><br>I tested out itkBFImageInfo
and ./itkRGBBioFormatsImageIOTest on a few simple LSM images. It works
great and writes out all the associated metadata and pixel data for the first timepoint. <br>
<br>My LSM microscopy image is 5D. It is X-Y-Z-Time-Channel. I am interested in extracting individual timepoints from the LSM file for processing. The filter seems to be using itkStreamingImageFilter. I set the NumberOfStreams
to 10 but that still seems to still write out only the first image. <br><br>How do I set the output requestion region for an individual timepoint?<br>
<br>Thank you,<br><br>Kishore
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