AW: openslide-users Digest, Vol 115, Issue 6
PD Dr. med. M. Weihrauch
m.weihrauch at smartinmedia.com
Fri Apr 10 13:07:31 EDT 2020
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 <jcortell at kanteron.com>
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 <m.weihrauch at smartinmedia.com>; jcupitt at gmail.com
Betreff: Re: openslide-users Digest, Vol 115, Issue 6
I agree with Derek.
My company (www.kanteron.com<http://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
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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 <D.R.Magee at leeds.ac.uk<mailto:D.R.Magee at leeds.ac.uk>>
To: "PD Dr. med. M. Weihrauch" <m.weihrauch at smartinmedia.com<mailto:m.weihrauch at smartinmedia.com>>,
"jcupitt at gmail.com<mailto:jcupitt at gmail.com>" <jcupitt at gmail.com<mailto:jcupitt at gmail.com>>
Cc: "openslide-users at lists.andrew.cmu.edu<mailto:openslide-users at lists.andrew.cmu.edu>"
<openslide-users at lists.andrew.cmu.edu<mailto:openslide-users at lists.andrew.cmu.edu>>
Subject: Re: openslide_read_region filling buffer with 0's for Mirax
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"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 <openslide-users-bounces+d.r.magee=leeds.ac.uk at lists.andrew.cmu.edu<mailto:leeds.ac.uk at lists.andrew.cmu.edu>> on behalf of PD Dr. med. M. Weihrauch <m.weihrauch at smartinmedia.com<mailto:m.weihrauch at smartinmedia.com>>
Sent: 10 April 2020 14:42
To: jcupitt at gmail.com<mailto:jcupitt at gmail.com> <jcupitt at gmail.com<mailto:jcupitt at gmail.com>>
Cc: openslide-users at lists.andrew.cmu.edu<mailto:openslide-users at lists.andrew.cmu.edu> <openslide-users at lists.andrew.cmu.edu<mailto: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 <openslide-users-bounces+m.weihrauch=smartinmedia.com at lists.andrew.cmu.edu<mailto:smartinmedia.com at lists.andrew.cmu.edu>> Im Auftrag von jcupitt at gmail.com<mailto:jcupitt at gmail.com>
Gesendet: Freitag, 10. April 2020 15:20
Cc: openslide-users at lists.andrew.cmu.edu<mailto: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<mailto:m.weihrauch at smartinmedia.com><mailto:m.weihrauch at smartinmedia.com<mailto: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<mailto:martin.weihrauch at uni-koeln.de><mailto:martin.weihrauch at uni-koeln.de<mailto:martin.weihrauch at uni-koeln.de>>>
Gesendet: Freitag, 10. April 2020 14:27
An: T. N. <ca95129 at hotmail.com<mailto:ca95129 at hotmail.com><mailto:ca95129 at hotmail.com<mailto:ca95129 at hotmail.com>>>; PD Dr. med. M. Weihrauch <m.weihrauch at smartinmedia.com<mailto:m.weihrauch at smartinmedia.com><mailto:m.weihrauch at smartinmedia.com<mailto:m.weihrauch at smartinmedia.com>>>; openslide-users at lists.andrew.cmu.edu<mailto:openslide-users at lists.andrew.cmu.edu><mailto:openslide-users at lists.andrew.cmu.edu<mailto: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." <ca95129 at hotmail.com<mailto:ca95129 at hotmail.com><mailto:ca95129 at hotmail.com<mailto:ca95129 at hotmail.com>>>
Datum: 10.04.20 13:35 (GMT+01:00)
An: "PD Dr. med. M. Weihrauch" <m.weihrauch at smartinmedia.com<mailto:m.weihrauch at smartinmedia.com><mailto:m.weihrauch at smartinmedia.com<mailto:m.weihrauch at smartinmedia.com>>>, openslide-users at lists.andrew.cmu.edu<mailto:openslide-users at lists.andrew.cmu.edu><mailto:openslide-users at lists.andrew.cmu.edu<mailto: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." <ca95129 at hotmail.com<mailto:ca95129 at hotmail.com>><mailto:ca95129 at hotmail.com<mailto:ca95129 at hotmail.com>>
Datum: 10.04.20 10:16 (GMT+01:00)
An: openslide-users at lists.andrew.cmu.edu<mailto:openslide-users at lists.andrew.cmu.edu><mailto:openslide-users at lists.andrew.cmu.edu<mailto: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
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