Philips Isyntax

Are there any plans to open Philips isyntax slides in QUPATH?
SDK https://www.openpathology.philips.com/downloads/

You might be interested in this thread.

@Gondim No, this is not something that can be resolved on the QuPath side. It is entirely up to Philips; as far as I can tell, their proprietary SDK is not compatible with QuPath’s open source license.

You’ll need to convert the files, e.g. with https://www.glencoesoftware.com/blog/2019/12/09/converting-whole-slide-images-to-OME-TIFF.html

See also the QuPath docs https://qupath.readthedocs.io/en/latest/docs/intro/formats.html#isyntax-philips

@Research_Associate @petebankhead Philips released more info today about isyntax . Would this change anything? https://twitter.com/Philips_Path/status/1262760508635004931

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Thanks for the link - very interesting, I didn’t know anything about it. I haven’t looked very closely, but if it is really open source-friendly then support in QuPath might become possible eventually.

Personally, I don’t have any iSyntax files and therefore it is not something I can/wish to work on myself any time soon. But if it could be supported in Bio-Formats, then QuPath (and many other projects) would benefit immediately.

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Hi Pete,
We would like to add Philips ISyntax Format to Qupath, went though some of QuPath links and understood that some work been done in past. Can you please provide some pointers how to achieve it / where to start for it? Philips now made its ISyntax format as open.

Thanks and Regards,
Kishore

Hi Kishore,

You could use any of the existing QuPath ImageServers as a starting point - there are separate modules in the QuPath code for several of these (OpenSlide, Bio-Formats, OMERO). These are all extensions, and so can be automatically discovered and loaded without needing to change anything within the main QuPath code.

However, it’s not entirely clear to me quite how ‘open’ the format is. I know the specifications are now online and some code; I haven’t looked at them in detail, but whether these can legitimately be integrated into other software without Philips’ explicit agreement is not clear to me. Without such agreement I personally wouldn’t want to include iSyntax support within QuPath directly.

My preference would still be to see iSyntax supported within a specialist image-reading library – which really means Bio-Formats (since as far as I’m aware OpenSlide is no longer actively maintained). The ‘post-processing for image viewing’ for iSyntax looks rather complex, and I think there is a risk that multiple implementations might be created that differ in some details. It would be wonderful to have an approved open source implementation available to both QuPath and other software.

Hi Pete,
Thanks for prompt reply. I work for Philips and interested in medical software especially Digital computational pathology and Bio-formats. Philips has made its ISyntax specification completely open and me happen to be one of the team member who worked for it :slight_smile:

Now out of interest / passion, would like to integrate ISyntax with community platform tools like Openslide , ASAP and / or QuPath etc, and after some search understood Qupath seems better option than Openslide as openslide seems not actively maintained.

I have access to ISyntax files, downloaded QuPath code from git and built it. It got build successfully . At this point of time thought to check with you for some pointers where to start experimenting with code for further experiments / understanding to include ISyntax as bio-format for Qupath.

Pardon me for not introducing myself and for not giving you the context in earlier post.

Thanks and Regards,
Kishore

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Ah, excellent!

If it’s an option to develop the reader for Bio-Formats, I think that would be best inasmuch as many software applications could benefit (not only QuPath). In that case, absolutely nothing would need to be done on the QuPath side beyond updating the version of Bio-Formats in a future release (which happens regularly anyway).

However, if you want to try adding a reader in QuPath directly then you’ll need to implement ImageServerBuilder and ImageServer classes, and register them as Java services (i.e. add a file in the META-INF directory). That’s really all that’s required; all three of the extensions I mentioned earlier show this in action.

If this is packaged up as a jar file, you can install it in any version of QuPath simply by dragging the jar onto the main Window and accepting the offer to copy it to the extensions directory.

(This assumes you are able to implement everything in Java. Native libraries are a lot more painful to deal with.)

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Hi Pete,
Thanks for the inputs, would like to try both options :slight_smile:

After your initial suggestion went through ImageServer class and got some idea about it, will experiment bit more .

Actually me more interested in generic reader which is your suggestion one, so that many application could use it. Could you please elaborate how can we design it / where to start? I know there are multiple ways for it, with the format in hand, checking for the best way so that many applications could benefit from it. Any link or info would be helpful…

Thanks again ,
Kishore

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Hi @kishutvn, as one example you may want to look at the Glencoe tools to convert iSyntax files into OME-TIFF. See: https://www.glencoesoftware.com/blog/2019/12/09/converting-whole-slide-images-to-OME-TIFF.html QuPath (and many other tools) can directly read OME-TIFF format.
Cheers, Damir

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Sure @dsudar , will check it up
Thank you ,
Kishore

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Great. I noticed that the code examples for both the iSyntax format and the compression algorithm are as Matlab scripts. Is there an open source C/C++, or Java implementation available for both, now that Philips has made these public? Ideally with a permissive license, of course :slight_smile:. Thanks!!
Damir

@dsudar , yes the code samples are of matlab scripts and as of now there is no plan to release C++ / Java code samples and to use C++, SDK is released which can be found at https://www.openpathology.philips.com/pathologysdk/
Thank you,
Kishore