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Dear Yuanyuan,
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<div class="">the bfopen function is designed to initialize a reader from a given file and open</div>
<div class="">all the pixel data stored in this image. As you mentioned, the limit of 2GB per plane</div>
<div class="">makes this function not adapted to whole-slide imaging.</div>
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<div class="">if you are using MATLAB, you should be able to use the low-level functions and</div>
<div class="">especially one of the signatures of bfGetPlane [1] allowing to retrieve a tile instead</div>
<div class="">of the full plane. Under the hood, this method effectively uses openBytes [2]</div>
<div class="">to retrieve a XY subset of the plane.</div>
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<div class="">For instance, the following code should return the first 512x512 tile of the first</div>
<div class="">plane in your Hamamatsu file:</div>
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<div class="">>> bfCheckJavaPath();</div>
<div class="">>> r= bfGetReader(‘/path/to/your/image.his’);</div>
<div class="">>> I = bfGetPlane(r, 1m 1, 1, 512, 512);</div>
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<div class="">Best,</div>
<div class="">Sebastien</div>
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<div class="">[1] <a href="https://github.com/openmicroscopy/bioformats/blob/v5.2.4/components/formats-gpl/matlab/bfGetPlane.m#L10" class="">https://github.com/openmicroscopy/bioformats/blob/v5.2.4/components/formats-gpl/matlab/bfGetPlane.m#L10</a> </div>
<div class="">[2] <a href="http://downloads.openmicroscopy.org/bio-formats/5.2.4/api/loci/formats/FormatReader.html#openBytes(int,%20byte%5B%5D,%20int,%20int,%20int,%20int)" class="">http://downloads.openmicroscopy.org/bio-formats/5.2.4/api/loci/formats/FormatReader.html#openBytes(int,%20byte[],%20int,%20int,%20int,%20int)</a> <br class="">
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<div class="">On 3 Nov 2016, at 15:54, Yuanyuan Jiang <<a href="mailto:Yuanyuan.jiang@tuebingen.mpg.de" class="">Yuanyuan.jiang@tuebingen.mpg.de</a>> wrote:</div>
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<div class="MsoNormal">Dear All,<o:p class=""></o:p></div>
<div class="MsoNormal"><o:p class=""> </o:p></div>
<div class="MsoNormal">I have a big stream data from the Hamamatsu sCMOS camera. The file size is more than 10GB and the format can be .BTF(big tiff) or the .HIS format (Hamamatsu format). I tried to use the bioformats library (bfopen) to load in the MATLAB
or the ImageJ, in both cases, the latest jar files are added to the path of the software.
<o:p class=""></o:p></div>
<div class="MsoNormal"><o:p class=""> </o:p></div>
<div class="MsoNormal">However, for the HIS format, it only read portion of the data. That is probably due to the memory restriction of the bioformats only read 2 GB
<o:p class=""></o:p></div>
<div class="MsoNormal"><span style="color:#1F497D" class=""> error(['Image plane too large. Only 2GB of data can be extracted '...<o:p class=""></o:p></span></div>
<div class="MsoNormal"><span style="color:#1F497D" class=""> 'at one time. You can workaround the problem by opening '...<o:p class=""></o:p></span></div>
<div class="MsoNormal"><span style="color:#1F497D" class=""> 'the plane in tiles.']);<o:p class=""></o:p></span></div>
<div class="MsoNormal">One suggest from the link <a href="http://www.openmicroscopy.org/site/support/bio-formats5.2/about/bug-reporting.html" class="">
http://www.openmicroscopy.org/site/support/bio-formats5.2/about/bug-reporting.html</a><o:p class=""></o:p></div>
<div class="MsoNormal">But I do not find any examples to use it : <span class="pre">
<span style="font-size:10.5pt;font-family:Consolas;color:#333333;letter-spacing:.1pt;background:white" class="">openBytes(int,</span></span><span class="apple-converted-space"><span style="font-size:10.5pt;font-family:Consolas;color:#333333;letter-spacing:.1pt;background:white" class=""> </span></span><span class="pre"><span style="font-size:10.5pt;font-family:Consolas;color:#333333;letter-spacing:.1pt;background:white" class="">int,int,</span></span><span class="apple-converted-space"><span style="font-size:10.5pt;font-family:Consolas;color:#333333;letter-spacing:.1pt;background:white" class=""> </span></span><span class="pre"><span style="font-size:10.5pt;font-family:Consolas;color:#333333;letter-spacing:.1pt;background:white" class="">int,</span></span><span class="apple-converted-space"><span style="font-size:10.5pt;font-family:Consolas;color:#333333;letter-spacing:.1pt;background:white" class=""> </span></span><span class="pre"><span style="font-size:10.5pt;font-family:Consolas;color:#333333;letter-spacing:.1pt;background:white" class="">int)</span></span><span class="apple-converted-space"><span style="font-size: 10.5pt; font-family: 'Lucida Sans Unicode', sans-serif; letter-spacing: -0.1pt; background-color: white; background-position: initial initial; background-repeat: initial initial;" class=""> </span></span></div>
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<div class="MsoNormal"><span class="apple-converted-space"><span style="font-size: 10.5pt; font-family: 'Lucida Sans Unicode', sans-serif; letter-spacing: -0.1pt; background-color: white; background-position: initial initial; background-repeat: initial initial;" class=""><o:p class=""> </o:p></span></span><span style="font-family: 'Lucida Sans Unicode', sans-serif; font-size: 10.5pt; letter-spacing: -0.1pt; background-color: white;" class="">If
I use the big tiff format, the bio-formats can read the small dataset, but the larger dataset (>4GB), there is error to ask the Java advanced Imaging, which I have no clue to install or include.</span></div>
<div class="MsoNormal"><o:p class=""> </o:p></div>
<div class="MsoNormal">Error using bfGetReader (line 84)<o:p class=""></o:p></div>
<div class="MsoNormal">Java exception occurred:<o:p class=""></o:p></div>
<div class="MsoNormal">loci.formats.MissingLibraryException: Java Advanced Imaging<o:p class=""></o:p></div>
<div class="MsoNormal">(JAI) is required to read some TIFF files. Please install JAI<o:p class=""></o:p></div>
<div class="MsoNormal">from <a href="https://jai.dev.java.net/" class="">https://jai.dev.java.net/</a><o:p class=""></o:p></div>
<div class="MsoNormal"><o:p class=""> </o:p></div>
<div class="MsoNormal"><o:p class=""> </o:p></div>
<div class="MsoNormal">Can someone help me to find a solution. Really thanks a lot.<o:p class=""></o:p></div>
<div class="MsoNormal"><o:p class=""> </o:p></div>
<div class="MsoNormal"><o:p class=""> </o:p></div>
<div class="MsoNormal">Best regards,<o:p class=""></o:p></div>
<div class="MsoNormal"><o:p class=""> </o:p></div>
<div class="MsoNormal">Yuanyuan<o:p class=""></o:p></div>
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