From ulrike at mail.nih.gov Thu Jan 14 11:07:11 2021 From: ulrike at mail.nih.gov (Wagner, Ulrike (NIH/NCI) [C]) Date: Thu, 14 Jan 2021 16:07:11 +0000 Subject: DICOM support Message-ID: Hi, Are there plans to include support for DICOM and/or DICOM dual-personality files in Openslide? Ulli [Text Frederick National Laboratory on a teal background] [LinkedIn icon] [Twitter icon] [Facebook icon] [Instagram icon] Ulrike (Ulli) Wagner | Project Manager Biomedical Informatics and Data Science (BIDS) [Phone icon] cell: 240-344-6828 [Email icon] ulli.wagner at fnlcr.nih.gov [Contractor] [Location icon] Post Office Box B, Frederick, MD 21702 [Link icon] frederick.cancer.gov The Frederick National Laboratory for Cancer Research is operated by Leidos Biomedical Research, Inc. for the National Cancer Institute. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... 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Name: image007.png Type: image/png Size: 660 bytes Desc: image007.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image008.png Type: image/png Size: 645 bytes Desc: image008.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image009.png Type: image/png Size: 745 bytes Desc: image009.png URL: From m.weihrauch at smartinmedia.com Sat Jan 30 16:18:59 2021 From: m.weihrauch at smartinmedia.com (Martin Weihrauch) Date: Sat, 30 Jan 2021 21:18:59 +0000 Subject: DICOM WSI Message-ID: Hi everyone! Does abyone have sample slides in DICOM WSI format? Best regards Martin Von meinem/meiner Galaxy gesendet -------- Urspr?ngliche Nachricht -------- Von: "Dr. M. Weihrauch" Datum: 10.04.20 14:27 (GMT+01:00) 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 ashish.sharma at emory.edu Sat Jan 30 17:47:35 2021 From: ashish.sharma at emory.edu (Sharma, Ashish) Date: Sat, 30 Jan 2021 22:47:35 +0000 Subject: [External] DICOM WSI In-Reply-To: References: Message-ID: There is a tool called diconizer that can take a wait file and create dicom variants Best, Ashish Get Outlook for iOS ________________________________ From: openslide-users on behalf of Martin Weihrauch Sent: Saturday, January 30, 2021 4:18:59 PM To: openslide-users at lists.andrew.cmu.edu Subject: [External] DICOM WSI Hi everyone! Does abyone have sample slides in DICOM WSI format? Best regards Martin Von meinem/meiner Galaxy gesendet -------- Urspr?ngliche Nachricht -------- Von: "Dr. M. Weihrauch" Datum: 10.04.20 14:27 (GMT+01:00) 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 ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). -------------- next part -------------- An HTML attachment was scrubbed... URL: From dclunie at dclunie.com Sun Jan 31 09:50:26 2021 From: dclunie at dclunie.com (=?UTF-8?Q?David_Clunie?=) Date: Sun, 31 Jan 2021 14:50:26 +0000 Subject: DICOM WSI In-Reply-To: References: <98bd9d76-df79-cbdd-cae8-8002ac994d69@dclunie.com> Message-ID: <0100017758ec70f1-e48b8bbc-84c9-4532-9b21-7dced3319789-000000@email.amazonses.com> Hi Martin See: ftp://medical.nema.org/MEDICAL/Dicom/DataSets/WG26/ These are not all perfectly DICOM compliant, since they have evolved over time as vendors and implementers have gained more experience with the format, but they may be useful as a starting point. See also: http://dicom.nema.org/Dicom/DICOMWSI/#ToolsAndActivities David Clunie (dclunie at dclunie.com) On 1/30/21 4:18 PM, Martin Weihrauch wrote: > Hi everyone! > > Does anyone have sample slides in DICOM WSI format? > > Best regards > > Martin From m.weihrauch at smartinmedia.com Sun Jan 31 12:47:12 2021 From: m.weihrauch at smartinmedia.com (Martin Weihrauch) Date: Sun, 31 Jan 2021 17:47:12 +0000 Subject: AW: DICOM WSI In-Reply-To: <0100017758ec70f1-e48b8bbc-84c9-4532-9b21-7dced3319789-000000@email.amazonses.com> References: <98bd9d76-df79-cbdd-cae8-8002ac994d69@dclunie.com> <0100017758ec70f1-e48b8bbc-84c9-4532-9b21-7dced3319789-000000@email.amazonses.com> Message-ID: Thank you very much I'll check it out. BTW: we created a free Converter (from all WSI) to the open SZI format (https://spreader.blob.core.windows.net/pathozoomconverter/PathoZoom%20Converter%20Setup.exe), but we wanted to add DICOM. Then, I can also share that software here, if of interest (unfortunately not open source as it uses the SDKs of the scanner vendors). Best regards Martin -----Urspr?ngliche Nachricht----- Von: openslide-users Im Auftrag von David Clunie Gesendet: Sonntag, 31. Januar 2021 15:50 An: openslide-users at lists.andrew.cmu.edu Betreff: Re: DICOM WSI Hi Martin See: ftp://medical.nema.org/MEDICAL/Dicom/DataSets/WG26/ These are not all perfectly DICOM compliant, since they have evolved over time as vendors and implementers have gained more experience with the format, but they may be useful as a starting point. See also: http://dicom.nema.org/Dicom/DICOMWSI/#ToolsAndActivities David Clunie (dclunie at dclunie.com) On 1/30/21 4:18 PM, Martin Weihrauch wrote: > Hi everyone! > > Does anyone have sample slides in DICOM WSI format? > > Best regards > > Martin _______________________________________________ openslide-users mailing list openslide-users at lists.andrew.cmu.edu https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users