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<p class="MsoNormal">Hi,</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">I have created a utility that provides a capability to convert from many vendor formats to the DICOM (supplement 145 now embodied in standard) media file format for VL Whole Slide Microscopy Images.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">The utility is for Windows only, and is available as a GUI and command line program. I have made available both the 32-bit (x86) and 64-bit (x64) variants at:</p>
<p class="MsoNormal"> </p>
<p class="MsoListParagraph" style="text-indent:-18.0pt"><span style="font-family:Symbol"><span style="">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><a href="https://s3-eu-west-1.amazonaws.com/uk-co-ffei-sierra/Downloads/SierraConverter_Setup_x86.exe">https://s3-eu-west-1.amazonaws.com/uk-co-ffei-sierra/Downloads/SierraConverter_Setup_x86.exe</a></p>
<p class="MsoListParagraph" style="text-indent:-18.0pt"><span style="font-family:Symbol"><span style="">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><a href="https://s3-eu-west-1.amazonaws.com/uk-co-ffei-sierra/Downloads/SierraConverter_Setup_x64.exe">https://s3-eu-west-1.amazonaws.com/uk-co-ffei-sierra/Downloads/SierraConverter_Setup_x64.exe</a></p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">You may also need to install the Microsoft Visual C++ 2010 runtime libraries as these are not currently installed with the application.</p>
<p class="MsoNormal"> </p>
<p class="MsoListParagraph" style="text-indent:-18.0pt"><span style="font-family:Symbol"><span style="">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><a href="http://www.microsoft.com/en-gb/download/details.aspx?id=8328">http://www.microsoft.com/en-gb/download/details.aspx?id=8328</a> (x86)</p>
<p class="MsoListParagraph" style="text-indent:-18.0pt"><span style="font-family:Symbol"><span style="">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><a href="http://www.microsoft.com/en-gb/download/details.aspx?id=13523">http://www.microsoft.com/en-gb/download/details.aspx?id=13523</a> (x64)</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">A user guide for the utility can be downloaded from <a href="https://s3-eu-west-1.amazonaws.com/uk-co-ffei-sierra/Downloads/SierraConverter_UserGuide.pdf">
https://s3-eu-west-1.amazonaws.com/uk-co-ffei-sierra/Downloads/SierraConverter_UserGuide.pdf</a>.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">The utility uses the OpenSlide library, and as it has been used for a viewer that I also developed (sorry, but I cannot make this available to you) and I needed that to be able to open the DICOM images that I had converted (and from other
sources), I modified the sources to allow me to do this. In due diligence I have made available the modified OpenSlide sources. These can be downloaded from
<a href="https://s3-eu-west-1.amazonaws.com/uk-co-ffei-sierra/Downloads/openslide_src.zip">
https://s3-eu-west-1.amazonaws.com/uk-co-ffei-sierra/Downloads/openslide_src.zip</a>.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">The sources include a new vendor driver ‘nema’ chosen as this is the body that oversees changes to the DICOM standard. There is also a new ‘ffei’ vendor driver for a format that we are using internally so this can be ignored.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Please note that the DICOM support in the OpenSlide library only opens the first image in the file-set. Also if you analyse the resulting file(s) from the conversion you will see that I have made some assumptions about the image orientation
relative to the DICOM standard. These may not always be correct as I have no other vendor originated file sets to check.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">I believe that the file set written by the converter is valid as I used the ‘dciodvfy’ utility written by David Clunie (<a href="http://www.dclunie.com">http://www.dclunie.com</a>) to check.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">I use the excellent (and free) Rubo DICOM parser to look inside the DICOM files generated (<a href="http://www.rubomedical.com/dicomparser">http://www.rubomedical.com/dicomparser</a>).</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Note that you will need an ICC profile in order to use the utility. However the utility does not check that it is a scanner profile, so you could just use a monitor profile. Several are available in the C:\Windows\System32\spool\drivers\color
folder on Windows machines. The file will be populated with whichever you choose, but is unlikely to be semantically ‘correct’ as a result if you do not have access to the original vendor’s ICC profile. Vendors such as Aperio embed theirs so you could try
extracting it with a hex editor or such.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">John Stevenson-Hoare</p>
<p class="MsoNormal"> </p>
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