<div dir="ltr">So I just tried the CMU-3 sample mrxs slide from the OpenSlide site and I am getting the exact same result ... openslide_read_region is filling in the supplied buffer with all zeros. Has anyone been able to use OpenSlide with this particular demo case? I was certainly trying to avoid building a debug version of the OpenSlide library to start stepping through the code ... hopefully someone has successfully used the C library to read an Mirax slide?<div><br></div><div>I did download the 3DHistech viewer and sure enough it was able to view the various mrxs slides, however, I did not see any reference to an SDK that I could download ... can someone provide a link to that?</div><div><br></div><div>I also tried playing around with their converter ... when I converted MRXS to MRXS, it generated the corresponding data files and directory but I didn't see any new 'mrxs' file being created ... so wasn't able to try OpenSlide on the converted slide ... any ideas on that?</div><div><br></div><div>Ultimately, I am still hoping that I can read these files using only the OpenSlide library ... I will start looking at building my own version of the library to debug next but I am REALLY hoping someone has an answer before I have to resort to that!</div><div><br></div><div>Thanks,</div><div><br></div><div>Terry</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Apr 10, 2020 at 11:42 AM Derek Magee <<a href="mailto:D.R.Magee@leeds.ac.uk">D.R.Magee@leeds.ac.uk</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
"<span style="color:rgb(32,31,30);font-family:Calibri,sans-serif;font-size:14.6667px;background-color:rgb(255,255,255);display:inline">no pathologist will ever invest due to lack of return of investment"</span></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
For info we've digitised out entire clinical workflow in Leeds UK (1000+ slides/day) using ~6 Leica-Aperio scanners (they will be replaced by 3 higher capacity ones soon). There are a number of other institutions around the world that have done the same (Granada
in Spain, Coventry in UK, The whole of Sweden, Some institutions in the Netherlands etc.). Most are using either Leica-Aperio or Hammamatsu scanners, and propriety formats. There are a few Phillips clinical sites coming online also. There is even the odd institute
using DICOM. This is definitely the way forward for image standardisation. We're in a lot of discussions with various parties regarding DICOM for Digital Pathology and I can tell you it's a matter of when, not if, this will be supported by all the major
scanner vendors as a native format. If people are interested (probably when the COVID thing is all over) we have been sharing our experiences of this via various courses and publications. If people are interested I can put you in touch with the appropriate
people.</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
BTW Metasystems (German company) have had a robot slide loader for 15 years I'd say. It works with a regular microscope with a motorised stage. I think you'd be impressed with that also. It approaches the throughput of a dedicated slide scanner these days,
and the system is only around E10-20K (not including the microscope)</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Derek </div>
<div id="gmail-m_1619671594838166500appendonsend"></div>
<hr style="display:inline-block;width:98%">
<div id="gmail-m_1619671594838166500divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> openslide-users <openslide-users-bounces+d.r.magee=<a href="mailto:leeds.ac.uk@lists.andrew.cmu.edu" target="_blank">leeds.ac.uk@lists.andrew.cmu.edu</a>> on behalf of PD Dr. med. M. Weihrauch <<a href="mailto:m.weihrauch@smartinmedia.com" target="_blank">m.weihrauch@smartinmedia.com</a>><br>
<b>Sent:</b> 10 April 2020 14:42<br>
<b>To:</b> <a href="mailto:jcupitt@gmail.com" target="_blank">jcupitt@gmail.com</a> <<a href="mailto:jcupitt@gmail.com" target="_blank">jcupitt@gmail.com</a>><br>
<b>Cc:</b> <a href="mailto:openslide-users@lists.andrew.cmu.edu" target="_blank">openslide-users@lists.andrew.cmu.edu</a> <<a href="mailto:openslide-users@lists.andrew.cmu.edu" target="_blank">openslide-users@lists.andrew.cmu.edu</a>><br>
<b>Subject:</b> AW: openslide_read_region filling buffer with 0's for Mirax</font>
<div> </div>
</div>
<div lang="DE">
<div>
<p><span lang="EN-US">The truth is (for Germany) that most scanners sold are still for isolated research projects. Digital pathology as a “complete digitalization” of a diagnostic pathology institute is not yet happening. However,
the “game” is slowly starting now and there will be pressure coming from the doctors as soon as they want to interact with colleagues hitting a brick wall of vendor formats.</span></p>
<p><span lang="EN-US">I know that some of the vendors already have a hard time selling their scanners due to bad (non-open) formats.
</span></p>
<p><span lang="EN-US"> </span></p>
<p><span lang="EN-US">There are some great developments though (not yet marketing). One engineer husband of a dermatopathologist now builds his own scanners with a Kuka robot arm in between loading them. When I first saw this, I
could not speak for 10 minutes – it really was like this first iphone moment. </span>
</p>
<p><span lang="EN-US"> </span></p>
<p><span lang="EN-US">After having scruitinized all available scanners on the market he quickly saw that NONE of them was ready for digitalizing 1,000 slides per day. Most scanner vendors do the same mistake: all 1,000 slides queue
in front of only one objective. Or you buy 3 scanners (a 250,000€) to speed up the process, which no pathologist will ever invest due to lack of return of investment. Thus, he took his wife’s fate into his own hand and started constructing scanners. I really
hope his small company will succeed.</span></p>
<p><span lang="EN-US"> </span></p>
<p><span lang="EN-US">This is super intriguing and I can share a video to anyone interested (you can email me personally).
</span></p>
<p><span lang="EN-US"> </span></p>
<p><span lang="EN-US">He is using – and John you will love this – the SZI format
</span><span lang="EN-US" style="font-family:"Segoe UI Emoji",sans-serif">😊</span><span lang="EN-US"></span></p>
<p><span lang="EN-US"> </span></p>
<p><span lang="EN-US">Hope, things will change for the better, my company is working hard on that.</span></p>
<p><span lang="EN-US"> </span></p>
<p><span lang="EN-US">Best</span></p>
<p><span lang="EN-US"> </span></p>
<p><span lang="EN-US"> </span></p>
<p><span lang="EN-US">Martin </span></p>
<p><span lang="EN-US"> </span></p>
<p><span lang="EN-US"> </span></p>
<p><span lang="EN-US"> </span></p>
<p><b>Von:</b> openslide-users <openslide-users-bounces+m.weihrauch=<a href="mailto:smartinmedia.com@lists.andrew.cmu.edu" target="_blank">smartinmedia.com@lists.andrew.cmu.edu</a>>
<b>Im Auftrag von </b><a href="mailto:jcupitt@gmail.com" target="_blank">jcupitt@gmail.com</a><br>
<b>Gesendet:</b> Freitag, 10. April 2020 15:20<br>
<b>Cc:</b> <a href="mailto:openslide-users@lists.andrew.cmu.edu" target="_blank">openslide-users@lists.andrew.cmu.edu</a><br>
<b>Betreff:</b> Re: openslide_read_region filling buffer with 0's for Mirax</p>
<p> </p>
<div>
<div>
<p>If people made good openslide support a "must have" feature when choosing a scanner, vendors might contribute code for their formats to the project, and perhaps even pay something towards maintenance.</p>
</div>
<div>
<p> </p>
</div>
<div>
<p>Unfortunately, it has not become a common requirement, and openslide is slowly becoming less relevant. I suspect vendors are (privately) delighted :(</p>
</div>
<div>
<p> </p>
</div>
<div>
<p>John</p>
</div>
<div>
<p> </p>
</div>
<div>
<p> </p>
</div>
<div>
<p> </p>
</div>
<div>
<p> </p>
</div>
</div>
<p> </p>
<div>
<div>
<p>On Fri, 10 Apr 2020 at 14:02, PD Dr. med. M. Weihrauch <<a href="mailto:m.weihrauch@smartinmedia.com" target="_blank">m.weihrauch@smartinmedia.com</a>> wrote:</p>
</div>
<blockquote style="border-top:none;border-right:none;border-bottom:none;border-left:1pt solid rgb(204,204,204);padding:0cm 0cm 0cm 6pt;margin-left:4.8pt;margin-right:0cm">
<div>
<div>
<p><span lang="EN-US">I just had a look at their SDK: There is C# and C++ parts, but everything is “.sln” = Visual Studio based. I guess, it’s all for Windows really.</span></p>
<p><span lang="EN-US"> </span></p>
<p><span lang="EN-US">God, when will all the vendors get real and implement one single common file format – radiology made that happen 100 years ago? It’s like a jungle getting crazier by each day. It also seems like they are all
competing, who can come up with an even worse format (Roche *.bif anyone? Different overlapping tile sizes of tiles with >1,000 pixels and an XML, which tells you how to rearrange that mess on the screen? / 3dHistech or Olympus with many files per slide, etc)…</span></p>
<p><span lang="EN-US">With better, faster and especially cheaper scanners, we could be 5 years in the future already.</span></p>
<p><span lang="EN-US"> </span></p>
<p><span lang="EN-US">Sorry for letting off steam here – totally off-topic
</span><span lang="EN-US" style="font-family:"Segoe UI Emoji",sans-serif">😉</span><span lang="EN-US">
</span></p>
<p><span lang="EN-US"> </span></p>
<p><span lang="EN-US">Martin</span></p>
<p><span lang="EN-US"> </span></p>
<div>
<div style="border-right:none currentcolor;border-bottom:none currentcolor;border-left:none currentcolor;border-top:1pt solid currentcolor;padding:3pt 0cm 0cm">
<p><b>Von:</b> Dr. M. Weihrauch <<a href="mailto:martin.weihrauch@uni-koeln.de" target="_blank">martin.weihrauch@uni-koeln.de</a>>
<br>
<b>Gesendet:</b> Freitag, 10. April 2020 14:27<br>
<b>An:</b> T. N. <<a href="mailto:ca95129@hotmail.com" target="_blank">ca95129@hotmail.com</a>>; PD Dr. med. M. Weihrauch <<a href="mailto:m.weihrauch@smartinmedia.com" target="_blank">m.weihrauch@smartinmedia.com</a>>;
<a href="mailto:openslide-users@lists.andrew.cmu.edu" target="_blank">openslide-users@lists.andrew.cmu.edu</a><br>
<b>Betreff:</b> Re: openslide_read_region filling buffer with 0's for Mirax</p>
</div>
</div>
<p> </p>
<div>
<p>I don't know. Their demo is in C#, but I doubt they are running .NET Core.</p>
</div>
<div>
<p> </p>
</div>
<div>
<p>I'll check once I havd the chance.</p>
</div>
<div>
<p> </p>
</div>
<div>
<p> </p>
</div>
<div>
<p> </p>
</div>
<div id="gmail-m_1619671594838166500x_gmail-m_-4011007549418840808composer_signature">
<div>
<p><span style="font-size:9.5pt;color:rgb(87,87,87)">Von meinem Samsung Galaxy Smartphone gesendet.</span></p>
</div>
</div>
<div>
<p> </p>
</div>
<div>
<p> </p>
</div>
<div>
<div>
<p><span style="color:black">-------- Ursprüngliche Nachricht --------</span></p>
</div>
<div>
<p><span style="color:black">Von: "T. N." <<a href="mailto:ca95129@hotmail.com" target="_blank">ca95129@hotmail.com</a>>
</span></p>
</div>
<div>
<p><span style="color:black">Datum: 10.04.20 13:35 (GMT+01:00)
</span></p>
</div>
<div>
<p><span style="color:black">An: "PD Dr. med. M. Weihrauch" <<a href="mailto:m.weihrauch@smartinmedia.com" target="_blank">m.weihrauch@smartinmedia.com</a>>,
<a href="mailto:openslide-users@lists.andrew.cmu.edu" target="_blank">openslide-users@lists.andrew.cmu.edu</a>
</span></p>
</div>
<div>
<p><span style="color:black">Betreff: Re: openslide_read_region filling buffer with 0's for Mirax
</span></p>
</div>
<div>
<p><span style="color:black"> </span></p>
</div>
</div>
<p>Does the SDK from 3DHistech work on Linux?</p>
<p>Thanks.<br>
thomas</p>
<div>
<p>On 4/10/2020 10:23 AM, PD Dr. med. M. Weihrauch wrote:</p>
</div>
<blockquote style="margin-top:5pt;margin-bottom:5pt">
<div>
<p>3dHistech can also give you there SDK. it is somewhat buggy, but reads all files..</p>
</div>
<div>
<p> </p>
</div>
<div>
<p>best </p>
</div>
<div>
<p> </p>
</div>
<div>
<p>Martin</p>
</div>
<div>
<p> </p>
</div>
<div>
<p> </p>
</div>
<div>
<p> </p>
</div>
<div id="gmail-m_1619671594838166500x_gmail-m_-4011007549418840808composer_signature">
<div>
<p><span style="font-size:9.5pt;color:rgb(87,87,87)">Von meinem Samsung Galaxy Smartphone gesendet.</span></p>
</div>
</div>
<div>
<p> </p>
</div>
<div>
<p> </p>
</div>
<div>
<p> </p>
</div>
<div>
<p>-------- Ursprüngliche Nachricht --------</p>
</div>
<div>
<p>Von: "T. N." <a href="mailto:ca95129@hotmail.com" target="_blank">
<ca95129@hotmail.com></a> </p>
</div>
<div>
<p>Datum: 10.04.20 10:16 (GMT+01:00) </p>
</div>
<div>
<p>An: <a href="mailto:openslide-users@lists.andrew.cmu.edu" target="_blank">
openslide-users@lists.andrew.cmu.edu</a> </p>
</div>
<div>
<p>Betreff: Re: openslide_read_region filling buffer with 0's for Mirax
</p>
</div>
<div>
<p> </p>
</div>
<div>
<p>I don't work with C interface, I just use the tools under Linux and recently have problem with the Mirax files generated by the new 3DHistech scanner. The new file format does contain some extra information that OpenSlide rejects or doesn't understand.
I read in other mailing lists that people have successfully use 3DHistech converter (free download from 3DHistech site) to convert from MIRAX format to MIRAX format (same format conversion) and can successfully use the converted file with OpenSlide. The converter
basically removes the extra overlapping information from the file, This is an extra step that needs to be done on the scanner PC. Is there possibility that OpenSlide library can be updated to avoid this conversion step, eg, skipping the overlapping information
in the new Mirax format.</p>
<p>Regards,<br>
Thomas</p>
<div>
<p>On 4/9/2020 11:21 PM, Terry Wilson wrote:</p>
</div>
<blockquote style="margin-top:5pt;margin-bottom:5pt">
<div>
<p>I am using the C interface to the windows version of OpenSlide. I have successfully used it to for a number of different formats, however, the same code does not appear to be working for Mirax slides. I am able to open the
slide and see the various properties, however, anytime I try calling openslide_read_region, it always just fills in the buffer with 0's. According to the documentation that is an indication of some error, however, calling openslide_get_error immediately after
just returns a null error object. </p>
<div>
<p> </p>
</div>
<div>
<p>I saw an older post from someone on this mailing list who seemed to have the exact same problem I am having with Mirax slides ... unfortunately they seemed to eventually get it working but had no idea what they changed to get
it to work. So I am looking for some suggestions on what to try. I have tried retrieving all the data for the entire level 0 using a tile size of 512x512 and they all seem to come back with 0's. I tried getting an entire higher level (level 6) with one
call but same result. I have also tried various different Mirax slides (including some of the demo ones from the OpenSlide site) The code is pretty simple:</p>
</div>
<div>
<p> </p>
</div>
<div>
<p>// Try reading a single tile</p>
</div>
<div>
<p>// x, y values start at 0,0 and increase based on the tile size</p>
</div>
<div>
<p>int size = 512;</p>
</div>
<div>
<p> </p>
</div>
<div>
<p style="margin-bottom:12pt">uint32_t *data = new uint32_t[size * size];<br>
<br>
openslide_read_region(openslide, data, x, y, 0, size, size);<br>
const char* err = openslide_get_error(openslide);<br>
if (err != NULL)<br>
{<br>
printf("error detected");<br>
}</p>
</div>
<div>
<p>I used openslide_get_property_names / openslide_get_property_value to dump out all the various metadata values for the slides ... is there some value in this metadata that I need to be accounting for (I assumed that the OpenSlide
library was already doing that)? Any suggestions on how to trouble shoot this problem would be greatly appreciated.</p>
</div>
<div>
<p> </p>
</div>
<div>
<p>Regards,</p>
</div>
<div>
<p> </p>
</div>
<div>
<p>Terry</p>
</div>
</div>
<p style="margin-bottom:12pt"> </p>
<pre>_______________________________________________</pre>
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