From jim.odonnell at pathai.com Tue May 9 12:18:15 2023 From: jim.odonnell at pathai.com (Jim O'Donnell) Date: Tue, 9 May 2023 12:18:15 -0400 Subject: DICOM support with properties Message-ID: I've been very excited to see the new support for DICOM that recently got merged! I'm working on a PR that will expose some of the openslide.* properties that we rely on, and I'm reaching out in advance. My plan is to infer openslide.mpp-x and openslide.mpp-y from SharedFunctionalGroupsSequence -> PixelMeasuresSequence -> PixelSpacing, and openslide.objective-power from ObjectiveLensPower. I'll cache these at each layer alongside the tile information and refer to the lowest layer for setting the props. In a separate PR I'd like to also expose openslide.associated.label and openslide.associated.macro. It looks like that should be fairly trivial as there's already code to identify those objects. Any feedback on this plan would be appreciated! Jim O'Donnell PathAI -- *Disclaimer: This email and any corresponding attachments may contain confidential information. If you're not the intended recipient, any copying, distribution, disclosure, or use of any information contained in the email or its attachments is strictly prohibited. If you believe to have received this email in error, please email security at pathai.com immediately, then destroy the email and any attachments without reading or saving.* -------------- next part -------------- An HTML attachment was scrubbed... URL: From bgilbert+openslide at cs.cmu.edu Tue May 9 22:26:53 2023 From: bgilbert+openslide at cs.cmu.edu (Benjamin Gilbert) Date: Tue, 9 May 2023 22:26:53 -0400 Subject: DICOM support with properties In-Reply-To: References: Message-ID: On Tue, May 9, 2023 at 8:37?PM Jim O'Donnell wrote: > I've been very excited to see the new support for DICOM that recently got merged! I'm working on a PR that will expose some of the openslide.* properties that we rely on, and I'm reaching out in advance. > > My plan is to infer openslide.mpp-x and openslide.mpp-y from SharedFunctionalGroupsSequence -> PixelMeasuresSequence -> PixelSpacing, and openslide.objective-power from ObjectiveLensPower. I'll cache these at each layer alongside the tile information and refer to the lowest layer for setting the props. > > In a separate PR I'd like to also expose openslide.associated.label and openslide.associated.macro. It looks like that should be fairly trivial as there's already code to identify those objects. Thanks for your interest! I think John Cupitt is also planning to work on adding property and associated image support, so it'd be good to coordinate your work with him, either here or in https://github.com/openslide/openslide/issues/142. Best, --Benjamin Gilbert From jcupitt at gmail.com Wed May 10 12:07:28 2023 From: jcupitt at gmail.com (jcupitt at gmail.com) Date: Wed, 10 May 2023 17:07:28 +0100 Subject: DICOM support with properties In-Reply-To: References: Message-ID: Hi Jim, DICOM support is being added under a project that's due to finish by the end of June. I think all the features you're planning are on the roadmap, so if you can wait until then, they should just happen. Label and macro work for 3dhistech now, and there's a PR in train for Leica support. I'm currently reworking the DICOM parser to improve performance for sparse tile images -- that should be another PR later this week or early next. My forks, in case you're interested in following or collaborating on development: https://github.com/jcupitt/libdicom https://github.com/jcupitt/openslide/ John On Wed, 10 May 2023 at 01:39, Jim O'Donnell wrote: > > I've been very excited to see the new support for DICOM that recently got merged! I'm working on a PR that will expose some of the openslide.* properties that we rely on, and I'm reaching out in advance. > > My plan is to infer openslide.mpp-x and openslide.mpp-y from SharedFunctionalGroupsSequence -> PixelMeasuresSequence -> PixelSpacing, and openslide.objective-power from ObjectiveLensPower. I'll cache these at each layer alongside the tile information and refer to the lowest layer for setting the props. > > In a separate PR I'd like to also expose openslide.associated.label and openslide.associated.macro. It looks like that should be fairly trivial as there's already code to identify those objects. > > Any feedback on this plan would be appreciated! > > Jim O'Donnell > PathAI > > Disclaimer: This email and any corresponding attachments may contain confidential information. If you're not the intended recipient, any copying, distribution, disclosure, or use of any information contained in the email or its attachments is strictly prohibited. If you believe to have received this email in error, please email security at pathai.com immediately, then destroy the email and any attachments without reading or saving._______________________________________________ > openslide-users mailing list > openslide-users at lists.andrew.cmu.edu > https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users From ludovic.bertsch at morehisto.ai Wed May 31 11:45:44 2023 From: ludovic.bertsch at morehisto.ai (Ludovic BERTSCH) Date: Wed, 31 May 2023 17:45:44 +0200 (CEST) Subject: MRXS failing to load Message-ID: <1825919119.287626.1685547944966@email.ionos.fr> An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 135585 bytes Desc: not available URL: From bgilbert+openslide at cs.cmu.edu Wed May 31 17:57:04 2023 From: bgilbert+openslide at cs.cmu.edu (Benjamin Gilbert) Date: Wed, 31 May 2023 17:57:04 -0400 Subject: MRXS failing to load In-Reply-To: <1825919119.287626.1685547944966@email.ionos.fr> References: <1825919119.287626.1685547944966@email.ionos.fr> Message-ID: On Wed, May 31, 2023 at 5:55?PM Ludovic BERTSCH < ludovic.bertsch at morehisto.ai> wrote: > I created the following issue: > https://github.com/openslide/openslide/issues/453 > > I was wondering if somebody could have a look at it... > I've replied in the bug. Best, --Benjamin Gilbert -------------- next part -------------- An HTML attachment was scrubbed... URL: