From twilson7755 at gmail.com Thu Apr 9 17:21:13 2020 From: twilson7755 at gmail.com (Terry Wilson) Date: Thu, 9 Apr 2020 17:21:13 -0400 Subject: openslide_read_region filling buffer with 0's for Mirax Message-ID: 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. 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: // Try reading a single tile // x, y values start at 0,0 and increase based on the tile size int size = 512; uint32_t *data = new uint32_t[size * size]; openslide_read_region(openslide, data, x, y, 0, size, size); const char* err = openslide_get_error(openslide); if (err != NULL) { printf("error detected"); } 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. Regards, Terry -------------- next part -------------- An HTML attachment was scrubbed... URL: From ca95129 at hotmail.com Fri Apr 10 04:15:20 2020 From: ca95129 at hotmail.com (T. N.) Date: Fri, 10 Apr 2020 10:15:20 +0200 Subject: openslide_read_region filling buffer with 0's for Mirax In-Reply-To: References: Message-ID: 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. Regards, Thomas On 4/9/2020 11:21 PM, Terry Wilson wrote: > 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. > > 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: > > // Try reading a single tile > // x, y values start at 0,0 and increase based on the tile size > int size = 512; > > uint32_t *data = new uint32_t[size * size]; > > openslide_read_region(openslide, data, x, y, 0, size, size); > const char* err = openslide_get_error(openslide); > if (err != NULL) > { > ? ? printf("error detected"); > } > > 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. > > Regards, > > Terry > > _______________________________________________ > openslide-users mailing list > openslide-users at lists.andrew.cmu.edu > https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.weihrauch at smartinmedia.com Fri Apr 10 04:23:32 2020 From: m.weihrauch at smartinmedia.com (PD Dr. med. M. Weihrauch) Date: Fri, 10 Apr 2020 08:23:32 +0000 Subject: openslide_read_region filling buffer with 0's for Mirax In-Reply-To: References: , Message-ID: 3dHistech can also give you there SDK. it is somewhat buggy, but reads all files.. best Martin Von meinem Samsung Galaxy Smartphone gesendet. -------- Urspr?ngliche Nachricht -------- Von: "T. N." Datum: 10.04.20 10:16 (GMT+01:00) An: openslide-users at lists.andrew.cmu.edu Betreff: Re: openslide_read_region filling buffer with 0's for Mirax 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. Regards, Thomas On 4/9/2020 11:21 PM, Terry Wilson wrote: 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. 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: // Try reading a single tile // x, y values start at 0,0 and increase based on the tile size int size = 512; uint32_t *data = new uint32_t[size * size]; openslide_read_region(openslide, data, x, y, 0, size, size); const char* err = openslide_get_error(openslide); if (err != NULL) { printf("error detected"); } 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. Regards, Terry _______________________________________________ openslide-users mailing list openslide-users at lists.andrew.cmu.edu https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From ca95129 at hotmail.com Fri Apr 10 07:35:16 2020 From: ca95129 at hotmail.com (T. N.) Date: Fri, 10 Apr 2020 13:35:16 +0200 Subject: openslide_read_region filling buffer with 0's for Mirax In-Reply-To: References: Message-ID: Does the SDK from 3DHistech work on Linux? Thanks. thomas On 4/10/2020 10:23 AM, PD Dr. med. M. Weihrauch wrote: > 3dHistech can also give you there SDK. it is somewhat buggy, but reads > all files.. > > best > > Martin > > > > Von meinem Samsung Galaxy Smartphone gesendet. > > > > -------- Urspr?ngliche Nachricht -------- > Von: "T. N." > Datum: 10.04.20 10:16 (GMT+01:00) > An: openslide-users at lists.andrew.cmu.edu > Betreff: Re: openslide_read_region filling buffer with 0's for Mirax > > 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. > > Regards, > Thomas > > On 4/9/2020 11:21 PM, Terry Wilson wrote: >> 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. >> >> 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: >> >> // Try reading a single tile >> // x, y values start at 0,0 and increase based on the tile size >> int size = 512; >> >> uint32_t *data = new uint32_t[size * size]; >> >> openslide_read_region(openslide, data, x, y, 0, size, size); >> const char* err = openslide_get_error(openslide); >> if (err != NULL) >> { >> ? ? printf("error detected"); >> } >> >> 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. >> >> Regards, >> >> Terry >> >> _______________________________________________ >> openslide-users mailing list >> openslide-users at lists.andrew.cmu.edu >> https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From martin.weihrauch at uni-koeln.de Fri Apr 10 08:27:06 2020 From: martin.weihrauch at uni-koeln.de (Dr. M. Weihrauch) Date: Fri, 10 Apr 2020 14:27:06 +0200 Subject: openslide_read_region filling buffer with 0's for Mirax In-Reply-To: Message-ID: <202004101227.03ACR7nw027973@smtp-auth.uni-koeln.de> I don't know. Their demo is in C#, but I doubt they are running .NET Core.I'll check once I havd the chance.Von meinem Samsung Galaxy Smartphone gesendet. -------- Urspr?ngliche Nachricht --------Von: "T. N." Datum: 10.04.20 13:35 (GMT+01:00) An: "PD Dr. med. M. Weihrauch" , openslide-users at lists.andrew.cmu.edu Betreff: Re: openslide_read_region filling buffer with 0's for Mirax Does the SDK from 3DHistech work on Linux? Thanks. thomas On 4/10/2020 10:23 AM, PD Dr. med. M. Weihrauch wrote: 3dHistech can also give you there SDK. it is somewhat buggy, but reads all files.. best? Martin Von meinem Samsung Galaxy Smartphone gesendet. -------- Urspr?ngliche Nachricht -------- Von: "T. N." Datum: 10.04.20 10:16 (GMT+01:00) An: openslide-users at lists.andrew.cmu.edu Betreff: Re: openslide_read_region filling buffer with 0's for Mirax 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. Regards, Thomas On 4/9/2020 11:21 PM, Terry Wilson wrote: 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. 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: // Try reading a single tile // x, y values start at 0,0 and increase based on the tile size int size = 512; uint32_t *data = new uint32_t[size * size]; openslide_read_region(openslide, data, x, y, 0, size, size); const char* err = openslide_get_error(openslide); if (err != NULL) { ? ? printf("error detected"); } 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. Regards, Terry _______________________________________________ openslide-users mailing list openslide-users at lists.andrew.cmu.edu https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.weihrauch at smartinmedia.com Fri Apr 10 09:02:29 2020 From: m.weihrauch at smartinmedia.com (PD Dr. med. M. Weihrauch) Date: Fri, 10 Apr 2020 13:02:29 +0000 Subject: AW: openslide_read_region filling buffer with 0's for Mirax In-Reply-To: <202004101227.03ACR7nw027973@smtp-auth.uni-koeln.de> References: <202004101227.03ACR7nw027973@smtp-auth.uni-koeln.de> Message-ID: 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. 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)? With better, faster and especially cheaper scanners, we could be 5 years in the future already. Sorry for letting off steam here ? totally off-topic ? Martin Von: Dr. M. Weihrauch Gesendet: Freitag, 10. April 2020 14:27 An: T. N. ; PD Dr. med. M. Weihrauch ; openslide-users at lists.andrew.cmu.edu Betreff: Re: openslide_read_region filling buffer with 0's for Mirax I don't know. Their demo is in C#, but I doubt they are running .NET Core. I'll check once I havd the chance. Von meinem Samsung Galaxy Smartphone gesendet. -------- Urspr?ngliche Nachricht -------- Von: "T. N." > Datum: 10.04.20 13:35 (GMT+01:00) An: "PD Dr. med. M. Weihrauch" >, openslide-users at lists.andrew.cmu.edu Betreff: Re: openslide_read_region filling buffer with 0's for Mirax Does the SDK from 3DHistech work on Linux? Thanks. thomas On 4/10/2020 10:23 AM, PD Dr. med. M. Weihrauch wrote: 3dHistech can also give you there SDK. it is somewhat buggy, but reads all files.. best Martin Von meinem Samsung Galaxy Smartphone gesendet. -------- Urspr?ngliche Nachricht -------- Von: "T. N." Datum: 10.04.20 10:16 (GMT+01:00) An: openslide-users at lists.andrew.cmu.edu Betreff: Re: openslide_read_region filling buffer with 0's for Mirax 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. Regards, Thomas On 4/9/2020 11:21 PM, Terry Wilson wrote: 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. 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: // Try reading a single tile // x, y values start at 0,0 and increase based on the tile size int size = 512; uint32_t *data = new uint32_t[size * size]; openslide_read_region(openslide, data, x, y, 0, size, size); const char* err = openslide_get_error(openslide); if (err != NULL) { printf("error detected"); } 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. Regards, Terry _______________________________________________ openslide-users mailing list openslide-users at lists.andrew.cmu.edu https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From jcupitt at gmail.com Fri Apr 10 09:19:35 2020 From: jcupitt at gmail.com (jcupitt at gmail.com) Date: Fri, 10 Apr 2020 14:19:35 +0100 Subject: openslide_read_region filling buffer with 0's for Mirax In-Reply-To: References: <202004101227.03ACR7nw027973@smtp-auth.uni-koeln.de> Message-ID: 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. Unfortunately, it has not become a common requirement, and openslide is slowly becoming less relevant. I suspect vendors are (privately) delighted :( John On Fri, 10 Apr 2020 at 14:02, PD Dr. med. M. Weihrauch < m.weihrauch at smartinmedia.com> wrote: > 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. > > > > 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)? > > With better, faster and especially cheaper scanners, we could be 5 years > in the future already. > > > > Sorry for letting off steam here ? totally off-topic ? > > > > Martin > > > > *Von:* Dr. M. Weihrauch > *Gesendet:* Freitag, 10. April 2020 14:27 > *An:* T. N. ; PD Dr. med. M. Weihrauch < > m.weihrauch at smartinmedia.com>; openslide-users at lists.andrew.cmu.edu > *Betreff:* Re: openslide_read_region filling buffer with 0's for Mirax > > > > I don't know. Their demo is in C#, but I doubt they are running .NET Core. > > > > I'll check once I havd the chance. > > > > > > > > Von meinem Samsung Galaxy Smartphone gesendet. > > > > > > -------- Urspr?ngliche Nachricht -------- > > Von: "T. N." > > Datum: 10.04.20 13:35 (GMT+01:00) > > An: "PD Dr. med. M. Weihrauch" , > openslide-users at lists.andrew.cmu.edu > > Betreff: Re: openslide_read_region filling buffer with 0's for Mirax > > > > Does the SDK from 3DHistech work on Linux? > > Thanks. > thomas > > On 4/10/2020 10:23 AM, PD Dr. med. M. Weihrauch wrote: > > 3dHistech can also give you there SDK. it is somewhat buggy, but reads all > files.. > > > > best > > > > Martin > > > > > > > > Von meinem Samsung Galaxy Smartphone gesendet. > > > > > > > > -------- Urspr?ngliche Nachricht -------- > > Von: "T. N." > > Datum: 10.04.20 10:16 (GMT+01:00) > > An: openslide-users at lists.andrew.cmu.edu > > Betreff: Re: openslide_read_region filling buffer with 0's for Mirax > > > > 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. > > Regards, > Thomas > > On 4/9/2020 11:21 PM, Terry Wilson wrote: > > 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. > > > > 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: > > > > // Try reading a single tile > > // x, y values start at 0,0 and increase based on the tile size > > int size = 512; > > > > uint32_t *data = new uint32_t[size * size]; > > openslide_read_region(openslide, data, x, y, 0, size, size); > const char* err = openslide_get_error(openslide); > if (err != NULL) > { > printf("error detected"); > } > > 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. > > > > Regards, > > > > Terry > > > > _______________________________________________ > > openslide-users mailing list > > openslide-users at lists.andrew.cmu.edu > > https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users > > _______________________________________________ > openslide-users mailing list > openslide-users at lists.andrew.cmu.edu > https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.weihrauch at smartinmedia.com Fri Apr 10 09:42:32 2020 From: m.weihrauch at smartinmedia.com (PD Dr. med. M. Weihrauch) Date: Fri, 10 Apr 2020 13:42:32 +0000 Subject: AW: openslide_read_region filling buffer with 0's for Mirax In-Reply-To: References: <202004101227.03ACR7nw027973@smtp-auth.uni-koeln.de> Message-ID: 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. I know that some of the vendors already have a hard time selling their scanners due to bad (non-open) formats. 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. 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. This is super intriguing and I can share a video to anyone interested (you can email me personally). He is using ? and John you will love this ? the SZI format ? Hope, things will change for the better, my company is working hard on that. Best Martin Von: openslide-users Im Auftrag von jcupitt at gmail.com Gesendet: Freitag, 10. April 2020 15:20 Cc: openslide-users at lists.andrew.cmu.edu Betreff: Re: openslide_read_region filling buffer with 0's for Mirax 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. Unfortunately, it has not become a common requirement, and openslide is slowly becoming less relevant. I suspect vendors are (privately) delighted :( John On Fri, 10 Apr 2020 at 14:02, PD Dr. med. M. Weihrauch > wrote: 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. 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)? With better, faster and especially cheaper scanners, we could be 5 years in the future already. Sorry for letting off steam here ? totally off-topic ? Martin Von: Dr. M. Weihrauch > Gesendet: Freitag, 10. April 2020 14:27 An: T. N. >; PD Dr. med. M. Weihrauch >; openslide-users at lists.andrew.cmu.edu Betreff: Re: openslide_read_region filling buffer with 0's for Mirax I don't know. Their demo is in C#, but I doubt they are running .NET Core. I'll check once I havd the chance. Von meinem Samsung Galaxy Smartphone gesendet. -------- Urspr?ngliche Nachricht -------- Von: "T. N." > Datum: 10.04.20 13:35 (GMT+01:00) An: "PD Dr. med. M. Weihrauch" >, openslide-users at lists.andrew.cmu.edu Betreff: Re: openslide_read_region filling buffer with 0's for Mirax Does the SDK from 3DHistech work on Linux? Thanks. thomas On 4/10/2020 10:23 AM, PD Dr. med. M. Weihrauch wrote: 3dHistech can also give you there SDK. it is somewhat buggy, but reads all files.. best Martin Von meinem Samsung Galaxy Smartphone gesendet. -------- Urspr?ngliche Nachricht -------- Von: "T. N." Datum: 10.04.20 10:16 (GMT+01:00) An: openslide-users at lists.andrew.cmu.edu Betreff: Re: openslide_read_region filling buffer with 0's for Mirax 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. Regards, Thomas On 4/9/2020 11:21 PM, Terry Wilson wrote: 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. 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: // Try reading a single tile // x, y values start at 0,0 and increase based on the tile size int size = 512; uint32_t *data = new uint32_t[size * size]; openslide_read_region(openslide, data, x, y, 0, size, size); const char* err = openslide_get_error(openslide); if (err != NULL) { printf("error detected"); } 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. Regards, Terry _______________________________________________ openslide-users mailing list openslide-users at lists.andrew.cmu.edu https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users _______________________________________________ openslide-users mailing list openslide-users at lists.andrew.cmu.edu https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.hudecek at nki.nl Fri Apr 10 10:55:26 2020 From: j.hudecek at nki.nl (j.hudecek at nki.nl) Date: Fri, 10 Apr 2020 14:55:26 +0000 Subject: openslide_read_region filling buffer with 0's for Mirax In-Reply-To: References: <202004101227.03ACR7nw027973@smtp-auth.uni-koeln.de> Message-ID: <81900_1586530532_03AEtUGY052501_9081a11d8b074d5aac3a5a9e72087a6d@EXCH-A01.nki.nl> Hi, I agree that the format situation is a mess. SZI is indeed great. Have you considered extending it to use WEBP? It could save half the space. Or other jpeg replacement. Regards, Jan Hudecek From: openslide-users [mailto:openslide-users-bounces+j.hudecek=nki.nl at lists.andrew.cmu.edu] On Behalf Of PD Dr. med. M. Weihrauch Sent: vrijdag 10 april 2020 15:43 To: jcupitt at gmail.com Cc: openslide-users at lists.andrew.cmu.edu Subject: AW: openslide_read_region filling buffer with 0's for Mirax 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. I know that some of the vendors already have a hard time selling their scanners due to bad (non-open) formats. 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. 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. This is super intriguing and I can share a video to anyone interested (you can email me personally). He is using ? and John you will love this ? the SZI format ? Hope, things will change for the better, my company is working hard on that. Best Martin Von: openslide-users Im Auftrag von jcupitt at gmail.com Gesendet: Freitag, 10. April 2020 15:20 Cc: openslide-users at lists.andrew.cmu.edu Betreff: Re: openslide_read_region filling buffer with 0's for Mirax 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. Unfortunately, it has not become a common requirement, and openslide is slowly becoming less relevant. I suspect vendors are (privately) delighted :( John On Fri, 10 Apr 2020 at 14:02, PD Dr. med. M. Weihrauch > wrote: 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. 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)? With better, faster and especially cheaper scanners, we could be 5 years in the future already. Sorry for letting off steam here ? totally off-topic ? Martin Von: Dr. M. Weihrauch > Gesendet: Freitag, 10. April 2020 14:27 An: T. N. >; PD Dr. med. M. Weihrauch >; openslide-users at lists.andrew.cmu.edu Betreff: Re: openslide_read_region filling buffer with 0's for Mirax I don't know. Their demo is in C#, but I doubt they are running .NET Core. I'll check once I havd the chance. Von meinem Samsung Galaxy Smartphone gesendet. -------- Urspr?ngliche Nachricht -------- Von: "T. N." > Datum: 10.04.20 13:35 (GMT+01:00) An: "PD Dr. med. M. Weihrauch" >, openslide-users at lists.andrew.cmu.edu Betreff: Re: openslide_read_region filling buffer with 0's for Mirax Does the SDK from 3DHistech work on Linux? Thanks. thomas On 4/10/2020 10:23 AM, PD Dr. med. M. Weihrauch wrote: 3dHistech can also give you there SDK. it is somewhat buggy, but reads all files.. best Martin Von meinem Samsung Galaxy Smartphone gesendet. -------- Urspr?ngliche Nachricht -------- Von: "T. N." Datum: 10.04.20 10:16 (GMT+01:00) An: openslide-users at lists.andrew.cmu.edu Betreff: Re: openslide_read_region filling buffer with 0's for Mirax 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. Regards, Thomas On 4/9/2020 11:21 PM, Terry Wilson wrote: 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. 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: // Try reading a single tile // x, y values start at 0,0 and increase based on the tile size int size = 512; uint32_t *data = new uint32_t[size * size]; openslide_read_region(openslide, data, x, y, 0, size, size); const char* err = openslide_get_error(openslide); if (err != NULL) { printf("error detected"); } 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. Regards, Terry _______________________________________________ openslide-users mailing list openslide-users at lists.andrew.cmu.edu https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users _______________________________________________ openslide-users mailing list openslide-users at lists.andrew.cmu.edu https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From D.R.Magee at leeds.ac.uk Fri Apr 10 11:40:45 2020 From: D.R.Magee at leeds.ac.uk (Derek Magee) Date: Fri, 10 Apr 2020 15:40:45 +0000 Subject: openslide_read_region filling buffer with 0's for Mirax In-Reply-To: References: <202004101227.03ACR7nw027973@smtp-auth.uni-koeln.de> , Message-ID: "no pathologist will ever invest due to lack of return of investment" 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. 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) Derek ________________________________ From: openslide-users on behalf of PD Dr. med. M. Weihrauch Sent: 10 April 2020 14:42 To: jcupitt at gmail.com Cc: openslide-users at lists.andrew.cmu.edu Subject: AW: openslide_read_region filling buffer with 0's for Mirax 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. I know that some of the vendors already have a hard time selling their scanners due to bad (non-open) formats. 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. 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. This is super intriguing and I can share a video to anyone interested (you can email me personally). He is using ? and John you will love this ? the SZI format ?? Hope, things will change for the better, my company is working hard on that. Best Martin Von: openslide-users Im Auftrag von jcupitt at gmail.com Gesendet: Freitag, 10. April 2020 15:20 Cc: openslide-users at lists.andrew.cmu.edu Betreff: Re: openslide_read_region filling buffer with 0's for Mirax 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. Unfortunately, it has not become a common requirement, and openslide is slowly becoming less relevant. I suspect vendors are (privately) delighted :( John On Fri, 10 Apr 2020 at 14:02, PD Dr. med. M. Weihrauch > wrote: 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. 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)? With better, faster and especially cheaper scanners, we could be 5 years in the future already. Sorry for letting off steam here ? totally off-topic ?? Martin Von: Dr. M. Weihrauch > Gesendet: Freitag, 10. April 2020 14:27 An: T. N. >; PD Dr. med. M. Weihrauch >; openslide-users at lists.andrew.cmu.edu Betreff: Re: openslide_read_region filling buffer with 0's for Mirax I don't know. Their demo is in C#, but I doubt they are running .NET Core. I'll check once I havd the chance. Von meinem Samsung Galaxy Smartphone gesendet. -------- Urspr?ngliche Nachricht -------- Von: "T. N." > Datum: 10.04.20 13:35 (GMT+01:00) An: "PD Dr. med. M. Weihrauch" >, openslide-users at lists.andrew.cmu.edu Betreff: Re: openslide_read_region filling buffer with 0's for Mirax Does the SDK from 3DHistech work on Linux? Thanks. thomas On 4/10/2020 10:23 AM, PD Dr. med. M. Weihrauch wrote: 3dHistech can also give you there SDK. it is somewhat buggy, but reads all files.. best Martin Von meinem Samsung Galaxy Smartphone gesendet. -------- Urspr?ngliche Nachricht -------- Von: "T. N." Datum: 10.04.20 10:16 (GMT+01:00) An: openslide-users at lists.andrew.cmu.edu Betreff: Re: openslide_read_region filling buffer with 0's for Mirax 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. Regards, Thomas On 4/9/2020 11:21 PM, Terry Wilson wrote: 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. 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: // Try reading a single tile // x, y values start at 0,0 and increase based on the tile size int size = 512; uint32_t *data = new uint32_t[size * size]; openslide_read_region(openslide, data, x, y, 0, size, size); const char* err = openslide_get_error(openslide); if (err != NULL) { printf("error detected"); } 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. Regards, Terry _______________________________________________ openslide-users mailing list openslide-users at lists.andrew.cmu.edu https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users _______________________________________________ openslide-users mailing list openslide-users at lists.andrew.cmu.edu https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From jcortell at kanteron.com Fri Apr 10 11:54:10 2020 From: jcortell at kanteron.com (Jorge Cortell) Date: Fri, 10 Apr 2020 17:54:10 +0200 Subject: openslide-users Digest, Vol 115, Issue 6 In-Reply-To: References: Message-ID: I agree with Derek. My company (www.kanteron.com) is vendor-neutral (we work with ALL scanners in the market) and our software turns all and any scanner output into DICOM. Some of our developers have been active/passive participants in openslide and other FLOSS efforts. We have customers in several countries (from Mexico to Thailand) using it for primary diagnosis for years, with hundreds of slides per day. When I hear "no pathologist will ever invest due to lack of return of investment" it makes me sad. That's a pathologist comparing looking into a microscope vs looking at a screen. BUT, how about all the other workflow actions around it? It's all about Transaction Cost: search for a slide (by patient name, or date), calculate how many types of staining per week, seek a second opinion or teleconsultation, participate in a Multidisciplinary Team (like Molecular Tumor Board), using thrid party advanced visualization algorithms, applying ML/AI/analytics, population health, teaching... when you consider the whole WORKFLOW (which our software provides, beyond just image transformation, visualization and reporting), then return on investment becomes VERY clear. My two cents. [Relevant] self-promotion out. Jorge Cortell Founder & CEO Kanteron Systems On Fri, Apr 10, 2020 at 5:42 PM < openslide-users-request at lists.andrew.cmu.edu> wrote: > Send openslide-users mailing list submissions to > openslide-users at lists.andrew.cmu.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users > or, via email, send a message with subject or body 'help' to > openslide-users-request at lists.andrew.cmu.edu > > You can reach the person managing the list at > openslide-users-owner at lists.andrew.cmu.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of openslide-users digest..." > > > Today's Topics: > > 1. Re: openslide_read_region filling buffer with 0's for Mirax > (Derek Magee) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 10 Apr 2020 15:40:45 +0000 > From: Derek Magee > To: "PD Dr. med. M. Weihrauch" , > "jcupitt at gmail.com" > Cc: "openslide-users at lists.andrew.cmu.edu" > > Subject: Re: openslide_read_region filling buffer with 0's for Mirax > Message-ID: > < > DB6PR03MB3109C2A65348A52EC720BE9AE0DE0 at DB6PR03MB3109.eurprd03.prod.outlook.com > > > > Content-Type: text/plain; charset="windows-1252" > > "no pathologist will ever invest due to lack of return of investment" > > 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 in! > terested I can put you in touch with the appropriate people. > > 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) > > Derek > ________________________________ > From: openslide-users leeds.ac.uk at lists.andrew.cmu.edu> on behalf of PD Dr. med. M. Weihrauch < > m.weihrauch at smartinmedia.com> > Sent: 10 April 2020 14:42 > To: jcupitt at gmail.com > Cc: openslide-users at lists.andrew.cmu.edu < > openslide-users at lists.andrew.cmu.edu> > Subject: AW: openslide_read_region filling buffer with 0's for Mirax > > > 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. > > I know that some of the vendors already have a hard time selling their > scanners due to bad (non-open) formats. > > > > 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. > > > > 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. > > > > This is super intriguing and I can share a video to anyone interested (you > can email me personally). > > > > He is using ? and John you will love this ? the SZI format ?? > > > > Hope, things will change for the better, my company is working hard on > that. > > > > Best > > > > > > Martin > > > > > > > > Von: openslide-users smartinmedia.com at lists.andrew.cmu.edu> Im Auftrag von jcupitt at gmail.com > Gesendet: Freitag, 10. April 2020 15:20 > Cc: openslide-users at lists.andrew.cmu.edu > Betreff: Re: openslide_read_region filling buffer with 0's for Mirax > > > > 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. > > > > Unfortunately, it has not become a common requirement, and openslide is > slowly becoming less relevant. I suspect vendors are (privately) delighted > :( > > > > John > > > > > > > > > > > > On Fri, 10 Apr 2020 at 14:02, PD Dr. med. M. Weihrauch < > m.weihrauch at smartinmedia.com> wrote: > > 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. > > > > 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)? > > With better, faster and especially cheaper scanners, we could be 5 years > in the future already. > > > > Sorry for letting off steam here ? totally off-topic ?? > > > > Martin > > > > Von: Dr. M. Weihrauch martin.weihrauch at uni-koeln.de>> > Gesendet: Freitag, 10. April 2020 14:27 > An: T. N. >; PD Dr. med. > M. Weihrauch m.weihrauch at smartinmedia.com>>; openslide-users at lists.andrew.cmu.edu > > Betreff: Re: openslide_read_region filling buffer with 0's for Mirax > > > > I don't know. Their demo is in C#, but I doubt they are running .NET Core. > > > > I'll check once I havd the chance. > > > > > > > > Von meinem Samsung Galaxy Smartphone gesendet. > > > > > > -------- Urspr?ngliche Nachricht -------- > > Von: "T. N." > > > Datum: 10.04.20 13:35 (GMT+01:00) > > An: "PD Dr. med. M. Weihrauch" m.weihrauch at smartinmedia.com>>, openslide-users at lists.andrew.cmu.edu > > > Betreff: Re: openslide_read_region filling buffer with 0's for Mirax > > > > Does the SDK from 3DHistech work on Linux? > > Thanks. > thomas > > On 4/10/2020 10:23 AM, PD Dr. med. M. Weihrauch wrote: > > 3dHistech can also give you there SDK. it is somewhat buggy, but reads all > files.. > > > > best > > > > Martin > > > > > > > > Von meinem Samsung Galaxy Smartphone gesendet. > > > > > > > > -------- Urspr?ngliche Nachricht -------- > > Von: "T. N." > > Datum: 10.04.20 10:16 (GMT+01:00) > > An: openslide-users at lists.andrew.cmu.edu openslide-users at lists.andrew.cmu.edu> > > Betreff: Re: openslide_read_region filling buffer with 0's for Mirax > > > > 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. > > Regards, > Thomas > > On 4/9/2020 11:21 PM, Terry Wilson wrote: > > 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. > > > > 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: > > > > // Try reading a single tile > > // x, y values start at 0,0 and increase based on the tile size > > int size = 512; > > > > uint32_t *data = new uint32_t[size * size]; > > openslide_read_region(openslide, data, x, y, 0, size, size); > const char* err = openslide_get_error(openslide); > if (err != NULL) > { > printf("error detected"); > } > > 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. > > > > Regards, > > > > Terry > > > > _______________________________________________ > > openslide-users mailing list > > openslide-users at lists.andrew.cmu.edu openslide-users at lists.andrew.cmu.edu> > > https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users > > _______________________________________________ > openslide-users mailing list > openslide-users at lists.andrew.cmu.edu openslide-users at lists.andrew.cmu.edu> > https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.andrew.cmu.edu/pipermail/openslide-users/attachments/20200410/01dffd53/attachment.html > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > openslide-users mailing list > openslide-users at lists.andrew.cmu.edu > https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users > > > ------------------------------ > > End of openslide-users Digest, Vol 115, Issue 6 > *********************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.weihrauch at smartinmedia.com Fri Apr 10 13:07:31 2020 From: m.weihrauch at smartinmedia.com (PD Dr. med. M. Weihrauch) Date: Fri, 10 Apr 2020 17:07:31 +0000 Subject: AW: openslide-users Digest, Vol 115, Issue 6 In-Reply-To: References: Message-ID: Thanks for your insight, guys! I mostly agree with you Derek and Jorge and you do a great job in pushing the borders to sth better! Again, I was talking about Germany and I meant: no (private) pathologist would currently buy 3 scanners a 250k?, which you would need to e. g. digitalize a lab with e. g. 3 pathologists, because you need to run them simultaneously to be as fast as without digital. In Germany, pathologists can have their own labs, so they are like a company (not sure how that compares to all the other countries) and have to watch their costs, too. One pathologist roughly works 50-100 cases per day, each case roughly 5 slides --> 250-500 slides per pathologist and day. Currently, they are relatively ?happy? with glass and digital does not add so much more advantages over digital ? compared to radiology (remember: in radiology, EVERY clinician like myself wants to look at the images, but in pathology, the clinicians don?t know what?s going on under the microscope ? so, in radiology, there was a need to ?multiply? the old films. Also, radiology films were expensive and CT slices on film are hard do diagnose, you need a magnifying glass). Scanning is (relatively) slow. So, let?s assume in a best case scenario, a scanner takes 1 minute per slide, then 1000 slides are 1000 minutes, which does not count loading the slides, etc. This is lost to the diagnostic speed compared with glass. Now, in Germany, you don?t get added money from the insurers, if you do anything digital. Also, the government doesn?t support it financially. Therefore, why should a lab currently buy scanners (so most of them think)? However (and that may be the case with your pathology, Derek?), at Universities, they sometimes do get funds from governments, etc to go digital. So, some Unis just get e. g. 1 million ? from the government/state and can buy scanners + software for their department. But there, no one ever looked at return of investment, because ? in a Uni ? they don?t have to. Again, the private pathologists (which are quite a lot) are still hesitant: because they have to make money. Therefore, we as a company rent out Hamamatsu scanners for e. g ?1,250/month and this is sometimes accepted by them and they do part-digitalization (e. g. 150 slides/day). I am 100% sure that everything will become digital, also in Germany, but this will take some more time here. Luckily, we are at the forefront with our products (wont post anything here as this group is not commercial). BTW: one really important aspect that most of the scanner companies are ignoring is that there is no need to scan everything at 40x. For the pathologist, it usually suffices to scan with a 10x objective (which almost mimics what they see with their eyes through a 20x) for 90% of the diagnoses. The technician could scan everything at 10x (except gastric biopsies for H pylori at 40x) and then, the pathologist can order a higher resolution if needed, just like ordering immunohistochemistry. Would massively speed up the process. Lastly, here is the video about the robot I mentioned. The cool thing is: you just slide down the staining trays in that aluminum sleigh and the slides are automatically ordered into cardboard boxes for storing: https://youtu.be/-fMYs-AxUcI Martin Von: Jorge Cortell Gesendet: Freitag, 10. April 2020 17:54 An: D.R.Magee at leeds.ac.uk Cc: openslide-users at lists.andrew.cmu.edu; PD Dr. med. M. Weihrauch ; jcupitt at gmail.com Betreff: Re: openslide-users Digest, Vol 115, Issue 6 I agree with Derek. My company (www.kanteron.com) is vendor-neutral (we work with ALL scanners in the market) and our software turns all and any scanner output into DICOM. Some of our developers have been active/passive participants in openslide and other FLOSS efforts. We have customers in several countries (from Mexico to Thailand) using it for primary diagnosis for years, with hundreds of slides per day. When I hear "no pathologist will ever invest due to lack of return of investment" it makes me sad. That's a pathologist comparing looking into a microscope vs looking at a screen. BUT, how about all the other workflow actions around it? It's all about Transaction Cost: search for a slide (by patient name, or date), calculate how many types of staining per week, seek a second opinion or teleconsultation, participate in a Multidisciplinary Team (like Molecular Tumor Board), using thrid party advanced visualization algorithms, applying ML/AI/analytics, population health, teaching... when you consider the whole WORKFLOW (which our software provides, beyond just image transformation, visualization and reporting), then return on investment becomes VERY clear. My two cents. [Relevant] self-promotion out. Jorge Cortell Founder & CEO Kanteron Systems On Fri, Apr 10, 2020 at 5:42 PM > wrote: Send openslide-users mailing list submissions to openslide-users at lists.andrew.cmu.edu To subscribe or unsubscribe via the World Wide Web, visit https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users or, via email, send a message with subject or body 'help' to openslide-users-request at lists.andrew.cmu.edu You can reach the person managing the list at openslide-users-owner at lists.andrew.cmu.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of openslide-users digest..." Today's Topics: 1. Re: openslide_read_region filling buffer with 0's for Mirax (Derek Magee) ---------------------------------------------------------------------- Message: 1 Date: Fri, 10 Apr 2020 15:40:45 +0000 From: Derek Magee > To: "PD Dr. med. M. Weihrauch" >, "jcupitt at gmail.com" > Cc: "openslide-users at lists.andrew.cmu.edu" > Subject: Re: openslide_read_region filling buffer with 0's for Mirax Message-ID: > Content-Type: text/plain; charset="windows-1252" "no pathologist will ever invest due to lack of return of investment" 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 in! terested I can put you in touch with the appropriate people. 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) Derek ________________________________ From: openslide-users > on behalf of PD Dr. med. M. Weihrauch > Sent: 10 April 2020 14:42 To: jcupitt at gmail.com > Cc: openslide-users at lists.andrew.cmu.edu > Subject: AW: openslide_read_region filling buffer with 0's for Mirax 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. I know that some of the vendors already have a hard time selling their scanners due to bad (non-open) formats. 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. 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. This is super intriguing and I can share a video to anyone interested (you can email me personally). He is using ? and John you will love this ? the SZI format ?? Hope, things will change for the better, my company is working hard on that. Best Martin Von: openslide-users > Im Auftrag von jcupitt at gmail.com Gesendet: Freitag, 10. April 2020 15:20 Cc: openslide-users at lists.andrew.cmu.edu Betreff: Re: openslide_read_region filling buffer with 0's for Mirax 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. Unfortunately, it has not become a common requirement, and openslide is slowly becoming less relevant. I suspect vendors are (privately) delighted :( John On Fri, 10 Apr 2020 at 14:02, PD Dr. med. M. Weihrauch >> wrote: 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. 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)? With better, faster and especially cheaper scanners, we could be 5 years in the future already. Sorry for letting off steam here ? totally off-topic ?? Martin Von: Dr. M. Weihrauch >> Gesendet: Freitag, 10. April 2020 14:27 An: T. N. >>; PD Dr. med. M. Weihrauch >>; openslide-users at lists.andrew.cmu.edu> Betreff: Re: openslide_read_region filling buffer with 0's for Mirax I don't know. Their demo is in C#, but I doubt they are running .NET Core. I'll check once I havd the chance. Von meinem Samsung Galaxy Smartphone gesendet. -------- Urspr?ngliche Nachricht -------- Von: "T. N." >> Datum: 10.04.20 13:35 (GMT+01:00) An: "PD Dr. med. M. Weihrauch" >>, openslide-users at lists.andrew.cmu.edu> Betreff: Re: openslide_read_region filling buffer with 0's for Mirax Does the SDK from 3DHistech work on Linux? Thanks. thomas On 4/10/2020 10:23 AM, PD Dr. med. M. Weihrauch wrote: 3dHistech can also give you there SDK. it is somewhat buggy, but reads all files.. best Martin Von meinem Samsung Galaxy Smartphone gesendet. -------- Urspr?ngliche Nachricht -------- Von: "T. N." >> Datum: 10.04.20 10:16 (GMT+01:00) An: openslide-users at lists.andrew.cmu.edu> Betreff: Re: openslide_read_region filling buffer with 0's for Mirax 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. Regards, Thomas On 4/9/2020 11:21 PM, Terry Wilson wrote: 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. 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: // Try reading a single tile // x, y values start at 0,0 and increase based on the tile size int size = 512; uint32_t *data = new uint32_t[size * size]; openslide_read_region(openslide, data, x, y, 0, size, size); const char* err = openslide_get_error(openslide); if (err != NULL) { printf("error detected"); } 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. Regards, Terry _______________________________________________ openslide-users mailing list openslide-users at lists.andrew.cmu.edu> https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users _______________________________________________ openslide-users mailing list openslide-users at lists.andrew.cmu.edu> https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Subject: Digest Footer _______________________________________________ openslide-users mailing list openslide-users at lists.andrew.cmu.edu https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users ------------------------------ End of openslide-users Digest, Vol 115, Issue 6 *********************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From twilson7755 at gmail.com Fri Apr 10 15:30:53 2020 From: twilson7755 at gmail.com (Terry Wilson) Date: Fri, 10 Apr 2020 15:30:53 -0400 Subject: openslide_read_region filling buffer with 0's for Mirax In-Reply-To: References: <202004101227.03ACR7nw027973@smtp-auth.uni-koeln.de> Message-ID: 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? 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? 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? 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! Thanks, Terry On Fri, Apr 10, 2020 at 11:42 AM Derek Magee wrote: > "no pathologist will ever invest due to lack of return of investment" > > 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. > > 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) > > Derek > ------------------------------ > *From:* openslide-users leeds.ac.uk at lists.andrew.cmu.edu> on behalf of PD Dr. med. M. Weihrauch < > m.weihrauch at smartinmedia.com> > *Sent:* 10 April 2020 14:42 > *To:* jcupitt at gmail.com > *Cc:* openslide-users at lists.andrew.cmu.edu < > openslide-users at lists.andrew.cmu.edu> > *Subject:* AW: openslide_read_region filling buffer with 0's for Mirax > > > 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. > > I know that some of the vendors already have a hard time selling their > scanners due to bad (non-open) formats. > > > > 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. > > > > 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. > > > > This is super intriguing and I can share a video to anyone interested (you > can email me personally). > > > > He is using ? and John you will love this ? the SZI format ? > > > > Hope, things will change for the better, my company is working hard on > that. > > > > Best > > > > > > Martin > > > > > > > > *Von:* openslide-users smartinmedia.com at lists.andrew.cmu.edu> *Im Auftrag von *jcupitt at gmail.com > *Gesendet:* Freitag, 10. April 2020 15:20 > *Cc:* openslide-users at lists.andrew.cmu.edu > *Betreff:* Re: openslide_read_region filling buffer with 0's for Mirax > > > > 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. > > > > Unfortunately, it has not become a common requirement, and openslide is > slowly becoming less relevant. I suspect vendors are (privately) delighted > :( > > > > John > > > > > > > > > > > > On Fri, 10 Apr 2020 at 14:02, PD Dr. med. M. Weihrauch < > m.weihrauch at smartinmedia.com> wrote: > > 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. > > > > 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)? > > With better, faster and especially cheaper scanners, we could be 5 years > in the future already. > > > > Sorry for letting off steam here ? totally off-topic ? > > > > Martin > > > > *Von:* Dr. M. Weihrauch > *Gesendet:* Freitag, 10. April 2020 14:27 > *An:* T. N. ; PD Dr. med. M. Weihrauch < > m.weihrauch at smartinmedia.com>; openslide-users at lists.andrew.cmu.edu > *Betreff:* Re: openslide_read_region filling buffer with 0's for Mirax > > > > I don't know. Their demo is in C#, but I doubt they are running .NET Core. > > > > I'll check once I havd the chance. > > > > > > > > Von meinem Samsung Galaxy Smartphone gesendet. > > > > > > -------- Urspr?ngliche Nachricht -------- > > Von: "T. N." > > Datum: 10.04.20 13:35 (GMT+01:00) > > An: "PD Dr. med. M. Weihrauch" , > openslide-users at lists.andrew.cmu.edu > > Betreff: Re: openslide_read_region filling buffer with 0's for Mirax > > > > Does the SDK from 3DHistech work on Linux? > > Thanks. > thomas > > On 4/10/2020 10:23 AM, PD Dr. med. M. Weihrauch wrote: > > 3dHistech can also give you there SDK. it is somewhat buggy, but reads all > files.. > > > > best > > > > Martin > > > > > > > > Von meinem Samsung Galaxy Smartphone gesendet. > > > > > > > > -------- Urspr?ngliche Nachricht -------- > > Von: "T. N." > > Datum: 10.04.20 10:16 (GMT+01:00) > > An: openslide-users at lists.andrew.cmu.edu > > Betreff: Re: openslide_read_region filling buffer with 0's for Mirax > > > > 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. > > Regards, > Thomas > > On 4/9/2020 11:21 PM, Terry Wilson wrote: > > 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. > > > > 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: > > > > // Try reading a single tile > > // x, y values start at 0,0 and increase based on the tile size > > int size = 512; > > > > uint32_t *data = new uint32_t[size * size]; > > openslide_read_region(openslide, data, x, y, 0, size, size); > const char* err = openslide_get_error(openslide); > if (err != NULL) > { > printf("error detected"); > } > > 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. > > > > Regards, > > > > Terry > > > > _______________________________________________ > > openslide-users mailing list > > openslide-users at lists.andrew.cmu.edu > > https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users > > _______________________________________________ > openslide-users mailing list > openslide-users at lists.andrew.cmu.edu > https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users > > _______________________________________________ > openslide-users mailing list > openslide-users at lists.andrew.cmu.edu > https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jcupitt at gmail.com Fri Apr 10 18:05:00 2020 From: jcupitt at gmail.com (jcupitt at gmail.com) Date: Fri, 10 Apr 2020 23:05:00 +0100 Subject: openslide_read_region filling buffer with 0's for Mirax In-Reply-To: References: <202004101227.03ACR7nw027973@smtp-auth.uni-koeln.de> Message-ID: On Fri, 10 Apr 2020 at 20:23, Terry Wilson wrote: > 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? > Yes, it works fine for me with Ubuntu 19.10 and their build of openslide. How did you build yours? Perhaps your jp2k decoder is not working? John -------------- next part -------------- An HTML attachment was scrubbed... URL: From twilson7755 at gmail.com Fri Apr 10 18:45:51 2020 From: twilson7755 at gmail.com (Terry Wilson) Date: Fri, 10 Apr 2020 18:45:51 -0400 Subject: openslide_read_region filling buffer with 0's for Mirax In-Reply-To: References: <202004101227.03ACR7nw027973@smtp-auth.uni-koeln.de> Message-ID: >> How did you build yours? Perhaps your jp2k decoder is not working? I didn't build my own, was just using the latest windows binaries (64 bit) available from the OpenSlide website (labelled 2017-11-22). Terry On Fri, Apr 10, 2020 at 6:05 PM wrote: > On Fri, 10 Apr 2020 at 20:23, Terry Wilson wrote: > >> 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? >> > > Yes, it works fine for me with Ubuntu 19.10 and their build of openslide. > > How did you build yours? Perhaps your jp2k decoder is not working? > > John > _______________________________________________ > openslide-users mailing list > openslide-users at lists.andrew.cmu.edu > https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ca95129 at hotmail.com Sat Apr 11 08:03:36 2020 From: ca95129 at hotmail.com (T. N.) Date: Sat, 11 Apr 2020 14:03:36 +0200 Subject: openslide_read_region filling buffer with 0's for Mirax In-Reply-To: References: <202004101227.03ACR7nw027973@smtp-auth.uni-koeln.de> Message-ID: > 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? Use the original .mrxs file with the converted data files (rename it to match your converted data folder name). T. -------------- next part -------------- An HTML attachment was scrubbed... URL: From twilson7755 at gmail.com Sun Apr 12 12:53:07 2020 From: twilson7755 at gmail.com (Terry Wilson) Date: Sun, 12 Apr 2020 12:53:07 -0400 Subject: openslide_read_region filling buffer with 0's for Mirax In-Reply-To: References: <202004101227.03ACR7nw027973@smtp-auth.uni-koeln.de> Message-ID: Using the original .mrxs file was the first thing I tried but it resulted in other errors being generated so I thought maybe there was something in that file that also needed to be changed. When using the original file with the generated data folder (of the same name), I am able to open the slide but calling any other openslide API results in a "Slide position file not of the expected size" error ... any ideas? So next I moved on to see if I could try and step through the code but ran into various issues: - I saw that the /bin folder of the openslide windows distribution included *.dll.debug files ... so I tried renaming all of these to just *.dll and run my application, however, it will not start up using these dll's, just crashes trying to load the application ... should these *.dll.debug files not work? - Even if the above did work, there are no PDB files so I'm guessing I can't debug this using Visual Studio? - Next tried to build my own openslide libraries following the instructions from the openslide site for building natively on windows (i.e. install cygwin, etc.). The build runs for a little while before crashing: - [ 63%] Linking C executable ../../../bin/opj_compress.exe collect2: fatal error: ld terminated with signal 11 [Segmentation fault], core dumped compilation terminated. make[2]: *** [src/bin/jp2/CMakeFiles/opj_compress.dir/build.make:205: bin/opj_compress.exe] Error 1 make[2]: *** Deleting file 'bin/opj_compress.exe' make[2]: Leaving directory '/cygdrive/d/Terry/openslide-winbuild-20171122/64/build/openjpeg-2.3.0' make[1]: *** [CMakeFiles/Makefile2:228: src/bin/jp2/CMakeFiles/opj_compress.dir/all] Error 2 make[1]: Leaving directory '/cygdrive/d/Terry/openslide-winbuild-20171122/64/build/openjpeg-2.3.0' make: *** [Makefile:152: all] Error 2 Failed: make $parallel (line 464) I would prefer NOT to have to build my own openslide libraries, so hopefully someone can let me know why my simple test app won't even start when trying to use the *.dll.debug dll's? Of course I would prefer if I didn't have to step through the code at all, but doesn't seem like I am going to be able to avoid that at this point :-( Thanks, Terry On Sat, Apr 11, 2020 at 8:03 AM T. N. wrote: > 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? > > Use the original .mrxs file with the converted data files (rename it to > match your converted data folder name). > > T. > > _______________________________________________ > openslide-users mailing list > openslide-users at lists.andrew.cmu.edu > https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jcupitt at gmail.com Sun Apr 12 13:30:21 2020 From: jcupitt at gmail.com (jcupitt at gmail.com) Date: Sun, 12 Apr 2020 18:30:21 +0100 Subject: openslide_read_region filling buffer with 0's for Mirax In-Reply-To: References: <202004101227.03ACR7nw027973@smtp-auth.uni-koeln.de> Message-ID: I help maintain an image processing package which includes openslide support. I just tried CMU-3.mrxs in the windows binary and it works for me. Try this: https://github.com/libvips/nip2/releases/download/v8.7.0/nip2-8.7.0-setup.zip Unzip and run the .exe to install. To load an MRXS file, click File / Open, navigate to the right directory, select "all files", and double-click on CMU-3.mrxs. It should load as a thumbnail in the workspace. Double-click the thumbnail to open an image view window. You should be able to scroll about and view the file. That's using the standard openslide sources, though I built them myself. You can sometimes get problems with special characters or spaces in the folder names, could that be it? John From twilson7755 at gmail.com Sun Apr 12 14:26:42 2020 From: twilson7755 at gmail.com (Terry Wilson) Date: Sun, 12 Apr 2020 14:26:42 -0400 Subject: openslide_read_region filling buffer with 0's for Mirax In-Reply-To: References: <202004101227.03ACR7nw027973@smtp-auth.uni-koeln.de> Message-ID: Yes I am able to successfully use your application to open various .mrxs files. Could you send me your libopenslide.lib file to see if I can build against your openslide libraries and run successfully? Thanks, Terry On Sun, Apr 12, 2020 at 1:31 PM wrote: > I help maintain an image processing package which includes openslide > support. I just tried CMU-3.mrxs in the windows binary and it works > for me. > > Try this: > > > https://github.com/libvips/nip2/releases/download/v8.7.0/nip2-8.7.0-setup.zip > > Unzip and run the .exe to install. To load an MRXS file, click File / > Open, navigate to the right directory, select "all files", and > double-click on CMU-3.mrxs. It should load as a thumbnail in the > workspace. Double-click the thumbnail to open an image view window. > You should be able to scroll about and view the file. > > That's using the standard openslide sources, though I built them myself. > > You can sometimes get problems with special characters or spaces in > the folder names, could that be it? > > John > _______________________________________________ > openslide-users mailing list > openslide-users at lists.andrew.cmu.edu > https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jcupitt at gmail.com Sun Apr 12 18:13:51 2020 From: jcupitt at gmail.com (jcupitt at gmail.com) Date: Sun, 12 Apr 2020 23:13:51 +0100 Subject: openslide_read_region filling buffer with 0's for Mirax In-Reply-To: References: <202004101227.03ACR7nw027973@smtp-auth.uni-koeln.de> Message-ID: The libvips dev zip has the openslide DLLs and LIBs: https://github.com/libvips/libvips/releases/download/v8.9.1/vips-dev-w64-all-8.9.1.zip On Sun, 12 Apr 2020 at 19:26, Terry Wilson wrote: > > Yes I am able to successfully use your application to open various .mrxs files. Could you send me your libopenslide.lib file to see if I can build against your openslide libraries and run successfully? > > Thanks, > > Terry > > On Sun, Apr 12, 2020 at 1:31 PM wrote: >> >> I help maintain an image processing package which includes openslide >> support. I just tried CMU-3.mrxs in the windows binary and it works >> for me. >> >> Try this: >> >> https://github.com/libvips/nip2/releases/download/v8.7.0/nip2-8.7.0-setup.zip >> >> Unzip and run the .exe to install. To load an MRXS file, click File / >> Open, navigate to the right directory, select "all files", and >> double-click on CMU-3.mrxs. It should load as a thumbnail in the >> workspace. Double-click the thumbnail to open an image view window. >> You should be able to scroll about and view the file. >> >> That's using the standard openslide sources, though I built them myself. >> >> You can sometimes get problems with special characters or spaces in >> the folder names, could that be it? >> >> John >> _______________________________________________ >> openslide-users mailing list >> openslide-users at lists.andrew.cmu.edu >> https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users From twilson7755 at gmail.com Sun Apr 12 22:40:24 2020 From: twilson7755 at gmail.com (Terry Wilson) Date: Sun, 12 Apr 2020 22:40:24 -0400 Subject: openslide_read_region filling buffer with 0's for Mirax In-Reply-To: References: <202004101227.03ACR7nw027973@smtp-auth.uni-koeln.de> Message-ID: Thanks for the zip file ... even using these lib's and dll's, the buffer is still being written with all 0's. If I could ask you one last favor and try this very simple program on your windows system and let me know what you see. #include "d:\openslide-win64-20171122\include\openslide\openslide.h" int main() { const char* fn = "C:\\Data\\CMU-3.mrxs"; openslide_t* openslide = openslide_open(fn); uint32_t *data = new uint32_t[512 * 512]; openslide_read_region(openslide, data, 0, 0, 0, 512, 512); for (int j = 0; j < 10; ++j) { printf("%x,", data[j]); } return 0; } Regards, Terry On Sun, Apr 12, 2020 at 6:14 PM wrote: > The libvips dev zip has the openslide DLLs and LIBs: > > > https://github.com/libvips/libvips/releases/download/v8.9.1/vips-dev-w64-all-8.9.1.zip > > On Sun, 12 Apr 2020 at 19:26, Terry Wilson wrote: > > > > Yes I am able to successfully use your application to open various .mrxs > files. Could you send me your libopenslide.lib file to see if I can build > against your openslide libraries and run successfully? > > > > Thanks, > > > > Terry > > > > On Sun, Apr 12, 2020 at 1:31 PM wrote: > >> > >> I help maintain an image processing package which includes openslide > >> support. I just tried CMU-3.mrxs in the windows binary and it works > >> for me. > >> > >> Try this: > >> > >> > https://github.com/libvips/nip2/releases/download/v8.7.0/nip2-8.7.0-setup.zip > >> > >> Unzip and run the .exe to install. To load an MRXS file, click File / > >> Open, navigate to the right directory, select "all files", and > >> double-click on CMU-3.mrxs. It should load as a thumbnail in the > >> workspace. Double-click the thumbnail to open an image view window. > >> You should be able to scroll about and view the file. > >> > >> That's using the standard openslide sources, though I built them myself. > >> > >> You can sometimes get problems with special characters or spaces in > >> the folder names, could that be it? > >> > >> John > >> _______________________________________________ > >> openslide-users mailing list > >> openslide-users at lists.andrew.cmu.edu > >> https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users > _______________________________________________ > openslide-users mailing list > openslide-users at lists.andrew.cmu.edu > https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jcupitt at gmail.com Sun Apr 12 23:10:06 2020 From: jcupitt at gmail.com (jcupitt at gmail.com) Date: Mon, 13 Apr 2020 04:10:06 +0100 Subject: openslide_read_region filling buffer with 0's for Mirax In-Reply-To: References: <202004101227.03ACR7nw027973@smtp-auth.uni-koeln.de> Message-ID: I tried and I think it's just because there's no data there. Try: openslide_read_region( openslide, data, 20000, 110000, 0, 512, 512 ); openslide gives you cairo premultiplied ARGB, so 0 means fully transparent, ie. the background colour, ie. white. You need to read from somewhere with actual data. On Mon, 13 Apr 2020 at 03:40, Terry Wilson wrote: > > Thanks for the zip file ... even using these lib's and dll's, the buffer is still being written with all 0's. If I could ask you one last favor and try this very simple program on your windows system and let me know what you see. > > #include "d:\openslide-win64-20171122\include\openslide\openslide.h" > > int main() > { > const char* fn = "C:\\Data\\CMU-3.mrxs"; > openslide_t* openslide = openslide_open(fn); > > uint32_t *data = new uint32_t[512 * 512]; > openslide_read_region(openslide, data, 0, 0, 0, 512, 512); > for (int j = 0; j < 10; ++j) > { > printf("%x,", data[j]); > } > > return 0; > } > > > Regards, > > Terry > > On Sun, Apr 12, 2020 at 6:14 PM wrote: >> >> The libvips dev zip has the openslide DLLs and LIBs: >> >> https://github.com/libvips/libvips/releases/download/v8.9.1/vips-dev-w64-all-8.9.1.zip >> >> On Sun, 12 Apr 2020 at 19:26, Terry Wilson wrote: >> > >> > Yes I am able to successfully use your application to open various .mrxs files. Could you send me your libopenslide.lib file to see if I can build against your openslide libraries and run successfully? >> > >> > Thanks, >> > >> > Terry >> > >> > On Sun, Apr 12, 2020 at 1:31 PM wrote: >> >> >> >> I help maintain an image processing package which includes openslide >> >> support. I just tried CMU-3.mrxs in the windows binary and it works >> >> for me. >> >> >> >> Try this: >> >> >> >> https://github.com/libvips/nip2/releases/download/v8.7.0/nip2-8.7.0-setup.zip >> >> >> >> Unzip and run the .exe to install. To load an MRXS file, click File / >> >> Open, navigate to the right directory, select "all files", and >> >> double-click on CMU-3.mrxs. It should load as a thumbnail in the >> >> workspace. Double-click the thumbnail to open an image view window. >> >> You should be able to scroll about and view the file. >> >> >> >> That's using the standard openslide sources, though I built them myself. >> >> >> >> You can sometimes get problems with special characters or spaces in >> >> the folder names, could that be it? >> >> >> >> John >> >> _______________________________________________ >> >> openslide-users mailing list >> >> openslide-users at lists.andrew.cmu.edu >> >> https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users >> _______________________________________________ >> openslide-users mailing list >> openslide-users at lists.andrew.cmu.edu >> https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users From twilson7755 at gmail.com Sun Apr 12 23:38:49 2020 From: twilson7755 at gmail.com (Terry Wilson) Date: Sun, 12 Apr 2020 23:38:49 -0400 Subject: openslide_read_region filling buffer with 0's for Mirax In-Reply-To: References: <202004101227.03ACR7nw027973@smtp-auth.uni-koeln.de> Message-ID: THANK YOU, I was able to read some non-zero data at that location ... I was not aware that the data had alpha applied, I just knew black tiles were not correct. Is it a reasonable assumption that the alpha value is either 0x00 or 0xff and not some partial values? Regards, Terry On Sun, Apr 12, 2020 at 11:10 PM wrote: > I tried and I think it's just because there's no data there. Try: > > openslide_read_region( openslide, data, 20000, 110000, 0, 512, 512 > ); > > openslide gives you cairo premultiplied ARGB, so 0 means fully > transparent, ie. the background colour, ie. white. You need to read > from somewhere with actual data. > > > On Mon, 13 Apr 2020 at 03:40, Terry Wilson wrote: > > > > Thanks for the zip file ... even using these lib's and dll's, the buffer > is still being written with all 0's. If I could ask you one last favor and > try this very simple program on your windows system and let me know what > you see. > > > > #include "d:\openslide-win64-20171122\include\openslide\openslide.h" > > > > int main() > > { > > const char* fn = "C:\\Data\\CMU-3.mrxs"; > > openslide_t* openslide = openslide_open(fn); > > > > uint32_t *data = new uint32_t[512 * 512]; > > openslide_read_region(openslide, data, 0, 0, 0, 512, 512); > > for (int j = 0; j < 10; ++j) > > { > > printf("%x,", data[j]); > > } > > > > return 0; > > } > > > > > > Regards, > > > > Terry > > > > On Sun, Apr 12, 2020 at 6:14 PM wrote: > >> > >> The libvips dev zip has the openslide DLLs and LIBs: > >> > >> > https://github.com/libvips/libvips/releases/download/v8.9.1/vips-dev-w64-all-8.9.1.zip > >> > >> On Sun, 12 Apr 2020 at 19:26, Terry Wilson > wrote: > >> > > >> > Yes I am able to successfully use your application to open various > .mrxs files. Could you send me your libopenslide.lib file to see if I can > build against your openslide libraries and run successfully? > >> > > >> > Thanks, > >> > > >> > Terry > >> > > >> > On Sun, Apr 12, 2020 at 1:31 PM wrote: > >> >> > >> >> I help maintain an image processing package which includes openslide > >> >> support. I just tried CMU-3.mrxs in the windows binary and it works > >> >> for me. > >> >> > >> >> Try this: > >> >> > >> >> > https://github.com/libvips/nip2/releases/download/v8.7.0/nip2-8.7.0-setup.zip > >> >> > >> >> Unzip and run the .exe to install. To load an MRXS file, click File / > >> >> Open, navigate to the right directory, select "all files", and > >> >> double-click on CMU-3.mrxs. It should load as a thumbnail in the > >> >> workspace. Double-click the thumbnail to open an image view window. > >> >> You should be able to scroll about and view the file. > >> >> > >> >> That's using the standard openslide sources, though I built them > myself. > >> >> > >> >> You can sometimes get problems with special characters or spaces in > >> >> the folder names, could that be it? > >> >> > >> >> John > >> >> _______________________________________________ > >> >> openslide-users mailing list > >> >> openslide-users at lists.andrew.cmu.edu > >> >> https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users > >> _______________________________________________ > >> openslide-users mailing list > >> openslide-users at lists.andrew.cmu.edu > >> https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users > _______________________________________________ > openslide-users mailing list > openslide-users at lists.andrew.cmu.edu > https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From grsuggitt at hotmail.com Mon Apr 6 14:44:51 2020 From: grsuggitt at hotmail.com (Gerry Suggitt) Date: Mon, 06 Apr 2020 18:44:51 -0000 Subject: OpenSlide in Linux-based Docker container running .Net Core Message-ID: I need to use OpenSlide in a Linux-based Docker Container. I have developed the application on Windows targeting .Net Core and it works when I launch it on my Windows machine. I have created the Docker Container but when I try to load the Windows x64 DLLs fromOpenSlide I get a "Bad IL format" error. I thought I could install the Debian version as I create the container but the command: RUN apt-get install openslide-tools gets the error: Unable to locate package openslide-tools The command '/bin/sh -c apt-get install openslide-tools' returned a non-zero code: 100 I am a n00b so please forgive me. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jj2883 at cumc.columbia.edu Sun Apr 12 23:37:37 2020 From: jj2883 at cumc.columbia.edu (Jang, Jun H.) Date: Mon, 13 Apr 2020 03:37:37 -0000 Subject: undefined reference to `__memcpy_chk' while building Openslide Message-ID: Hi, I am trying to build Openslide for Windows 10 64bit using Cygwin. I have followed the instructions in ReadMe file and I am keep running into the same error while building libpng. For Cygwin system, I currently have x86_64-w64-mingw32-gcc g++ 9.2.0 (for both) cmake 3.14.5 make 4.3 For python, I have python 3.7 (anaconda) installed on my system. So my question is: 1. To build Openslide, do I need Python installed on my computer? If so, how do I specify an environment that Cygwin can work with? 2. From what I am searching online and seeing in the command prompt, it seems like its most likely due to a version issue with the package version of programs such as make, cmake, mingw64 gcc, etc. Can someone provide me with a working versions of each necessary programs? * MinGW-w64 gcc and g++ for the target architecture (i686 or x86_64) * NASM * OpenJDK * Apache Ant * CMake * gettext utility programs * glib2 utility programs * Native gcc and binutils for your build platform 1. If it is not due to program versions, then can someone help me how to fix this error I am encountering? libtool: link: x86_64-w64-mingw32-gcc -static-libgcc -O2 -g -mms-bitfields -fexceptions -ftree-vectorize -static-libgcc -Wl,--enable-auto-image-base -Wl,--dynamicbase -Wl,--nxcompat -o .libs/png-fix-itxt.exe contrib/tools/png-fix-itxt.o -L/cygdrive/c/users/junhy/openslide2017/openslide-winbuild-20160612/64/root/lib -lz libtool: link: /usr/bin/x86_64-w64-mingw32-nm -B .libs/png.o .libs/pngerror.o .libs/pngget.o .libs/pngmem.o .libs/pngpread.o .libs/pngread.o .libs/pngrio.o .libs/pngrtran.o .libs/pngrutil.o .libs/pngset.o .libs/pngtrans.o .libs/pngwio.o .libs/pngwrite.o .libs/pngwtran.o .libs/pngwutil.o | sed -n -e 's/^.[ ]([ABCDGIRSTW][ABCDGIRSTW])[ ][ ]([_A-Za-z][_A-Za-z0-9])$/\1 \2 \2/p' | sed '/ __gnu_lto/d' | /usr/bin/sed -e '/^[BCDGRS][ ]/s/.[ ]([^ ])/\1 DATA/;s/^.[ ]nm([^ ])[ ][^ ]/\1 DATA/;/^I[ ]/d;/^[AITW][ ]/s/. //' | sort | uniq > .libs/libpng16.exp libtool: link: if test DEF = "/usr/bin/sed -n -e 's/^[ ]*//' -e '/^\(;.*\)*$/d' -e 's/^\(EXPORTS\|LIBRARY\)\([ ].*\)*$/DEF/p' -e q .libs/libpng16.def" ; then cp .libs/libpng16.def .libs/libpng16-16.dll.def; else echo EXPORTS > .libs/libpng16-16.dll.def; cat .libs/libpng16.def >> .libs/libpng16-16.dll.def; fi libtool: link: x86_64-w64-mingw32-gcc -static-libgcc -shared .libs/libpng16-16.dll.def .libs/png.o .libs/pngerror.o .libs/pngget.o .libs/pngmem.o .libs/pngpread.o .libs/pngread.o .libs/pngrio.o .libs/pngrtran.o .libs/pngrutil.o .libs/pngset.o .libs/pngtrans.o .libs/pngwio.o .libs/pngwrite.o .libs/pngwtran.o .libs/pngwutil.o -L/cygdrive/c/users/junhy/openslide2017/openslide-winbuild-20160612/64/root/lib -lz -O2 -g -mms-bitfields -Wl,--enable-auto-image-base -Wl,--dynamicbase -Wl,--nxcompat -o .libs/libpng16-16.dll -Wl,--enable-auto-image-base -Xlinker --out-implib -Xlinker .libs/libpng16.dll.a /usr/lib/gcc/x86_64-w64-mingw32/9.2.0/../../../../x86_64-w64-mingw32/bin/ld: .libs/pngrutil.o: in function memcpy': /usr/x86_64-w64-mingw32/sys-root/mingw/include/string.h:202: undefined reference to __memcpy_chk' /usr/lib/gcc/x86_64-w64-mingw32/9.2.0/../../../../x86_64-w64-mingw32/bin/ld: .libs/pngwutil.o: in function memcpy': /usr/x86_64-w64-mingw32/sys-root/mingw/include/string.h:202: undefined reference to __memcpy_chk' collect2: error: ld returned 1 exit status make[1]: *** [Makefile:869: libpng16.la] Error 1 make[1]: *** Waiting for unfinished jobs.... libtool: link: x86_64-w64-mingw32-gcc -static-libgcc -O2 -g -mms-bitfields -fexceptions -ftree-vectorize -static-libgcc -Wl,--enable-auto-image-base -Wl,--dynamicbase -Wl,--nxcompat -o .libs/png-fix-itxt.exe contrib/tools/png-fix-itxt.o -L/cygdrive/c/users/junhy/openslide2017/openslide-winbuild-20160612/64/root/lib -lz make[1]: Leaving directory '/cygdrive/c/users/junhy/openslide2017/openslide-winbuild-20160612/64/build/libpng-1.6.22' make: *** [Makefile:766: all] Error 2 Failed: make $parallel (line 401) Also, in regards to the last line of error: Failed: make $parallel (line 401) I have tried to change the number of parallels using -j 1 through 4, but it did not change the result. I have also tried building with 2017 release version, 2016 version, 2015 version, but they all give me the same error. In addition, I have tried to install Openslide in my windows linux subsystem (ubuntu16.04) and it worked fine. Thank you in advance. -Jun -------------- next part -------------- An HTML attachment was scrubbed... URL: