<div dir="ltr"><div><div><div>Hi Balaji,<br><br></div>Thanks for your suggestions. <br><br></div>To clarify my problem, we are dealing with <u>single images</u> with 182612 x 215608 pixels (~ 40 GPIX). As we are not dealing with a stack of images, as far as I am aware "extremely large image planes are not yet cached in ImageJ tilewise" <br><br>From what I have heard, "this is a future goal of the project"<br>
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* <a href="https://github.com/scifio/scifio/issues/125" target="_blank">https://github.com/scifio/scifio/issues/125</a><br>
* <a href="https://github.com/imagej/imagej/issues/87" target="_blank">https://github.com/imagej/imagej/issues/87</a><br><br></div>With respect to the work-around of cropping on import....as far as I understand, the current ImageJ plane limitation of 46340 x 46340 pixels (~2 GPIX) would require us to crop our image (182612 x 215608 pixels) (~40 GPIX) to approximately one twentieth its original size, which is obviously unacceptable. I suppose theoretically one could perform this operation twenty times, and if you were able to reconstruct the resulting image, this would be useful. However, this is well beyond my area of expertise. If anyone has a potential solution, it would be much appreciated. <br><br>Trevor<br><br></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Sep 10, 2014 at 1:36 PM, Balaji Ramalingam <span dir="ltr"><<a href="mailto:b.ramalingam@dundee.ac.uk" target="_blank">b.ramalingam@dundee.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div>Hi,</div>
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<div>Memory management is very important in such cases, and there are multiple ways to handle these files.</div>
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<div>The documentation for the same is given in here,</div>
<div><a href="http://www.openmicroscopy.org/site/support/bio-formats5/users/imagej/managing-memory.html" target="_blank">http://www.openmicroscopy.org/site/support/bio-formats5/users/imagej/managing-memory.html</a></div>
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<div>Please try the suggestions in here and let us know if the issue persists.</div>
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<div>Best,</div>
<div>Balaji</div>
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<div style="color:rgb(40,40,40)"><span style="background-color:rgb(255,255,255)">__________________</span></div>
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<p style="margin-top:0px;margin-bottom:0px">Mr Balaji Ramalingam</p>
<p style="margin-top:0px;margin-bottom:0px">Software Developer<br>
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<p style="margin-top:0px;margin-bottom:0px">OME Team</p>
<p style="margin-top:0px;margin-bottom:0px">College of Life Sciences</p>
<p style="margin-top:0px;margin-bottom:0px">University of Dundee</p>
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<span style="font-weight:bold">From: </span>Trevor Steve <<a href="mailto:tsteve@ualberta.ca" target="_blank">tsteve@ualberta.ca</a>><br>
<span style="font-weight:bold">Date: </span>Tuesday, 9 September 2014 17:51<br>
<span style="font-weight:bold">To: </span>"<a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a>" <<a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Subject: </span>[ome-users] Analyzing extremely large images from AxioScan/ZEN software<br>
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<div dir="ltr">Hi All,
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<div>I am attempting to analyze extremely large images produced on an AxioScan microscope and segmented using ZEN software. These are CZI files with JPEG-XR compression. </div>
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<div>Examples of my image sizes (pixels) are:</div>
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<div style="font-family:arial,sans-serif;font-size:12.8000001907349px">201276 X 203751</div>
<div style="font-family:arial,sans-serif;font-size:12.8000001907349px">205353 X 198345</div>
<div style="font-family:arial,sans-serif;font-size:12.8000001907349px">182611 X 215607</div>
<div style="font-family:arial,sans-serif;font-size:12.8000001907349px">167046 X 189615</div>
<div style="font-family:arial,sans-serif;font-size:12.8000001907349px">135139 X 188422</div>
<div style="font-family:arial,sans-serif;font-size:12.8000001907349px">158073 X 165835</div>
<div style="font-family:arial,sans-serif;font-size:12.8000001907349px">185008 X 144463</div>
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<div style="font-family:arial,sans-serif;font-size:12.8000001907349px"><br>
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<div style="font-family:arial,sans-serif;font-size:12.8000001907349px">When I run the .CZI to .TIF converter <a href="http://hcbi.fas.harvard.edu/resources_software" style="font-size:12.8000001907349px" target="_blank">http://hcbi.fas.harvard.edu/resources_software</a></div>
<div style="font-family:arial,sans-serif;font-size:12.8000001907349px">I end up with TIF files which are, as an example:</div>
<div style="font-family:arial,sans-serif;font-size:12.8000001907349px"><span style="font-size:12.8000001907349px">182612 x 215608 (> 39 GPIX), 74.3-80.2 GB</span><br>
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<div style="font-family:arial,sans-serif;font-size:12.8000001907349px"><span style="font-size:12.8000001907349px"><br>
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<div style="font-family:arial,sans-serif;font-size:12.8000001907349px"><span style="font-size:12.8000001907349px">These massive TIFF files cannot be opened by ImageJ (Bio-formats), Fiji, or Photoshop (CS5). </span><br>
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<div style="font-family:arial,sans-serif;font-size:12.8000001907349px"><span style="font-size:12.8000001907349px"><br>
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<div style="font-family:arial,sans-serif;font-size:12.8000001907349px"><span style="font-size:12.8000001907349px">I am wondering if anyone has found a solution to working with this type of data. Is it possible to reduce the resolution/size of the images produced
by the microscope/ZEN software?</span></div>
<div style="font-family:arial,sans-serif;font-size:12.8000001907349px"><span style="font-size:12.8000001907349px"><br>
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<div style="font-family:arial,sans-serif;font-size:12.8000001907349px"><span style="font-size:12.8000001907349px">Thanks, </span></div>
<div style="font-family:arial,sans-serif;font-size:12.8000001907349px"><span style="font-size:12.8000001907349px"><br>
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<div style="font-family:arial,sans-serif;font-size:12.8000001907349px"><span style="font-size:12.8000001907349px">Trevor</span></div>
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-- <br>
<div dir="ltr">Trevor Steve, MD
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<div>Neurology Resident (PGY-7)</div>
<div>PhD Student, Department of Medicine</div>
<div>University of Alberta</div>
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<span style="font-size:10pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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</blockquote></div><br><br clear="all"><br>-- <br><div dir="ltr">Trevor Steve, MD<div><br></div><div>Neurology Resident (PGY-7)</div><div>PhD Student, Department of Medicine</div><div>University of Alberta</div></div>
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