# Support for pathology DICOM

**URL:** <https://discourse.slicer.org/t/support-for-pathology-dicom/42248>\
**Category:** Development\
**Tags:** dicom, microscopy\
**Created:** [March 21, 2025, 4:22pm UTC](https://discourse.slicer.org/t/support-for-pathology-dicom/42248 "2025-03-21T16:22:39Z")\
**Posts on this page:** 12\
**Page:** 1

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**Author:** ![dzenanz](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/dzenanz/32/1992_2.png) [@dzenanz](https://discourse.slicer.org/u/dzenanz)\
**Post date:** [March 21, 2025, 4:22pm UTC](https://discourse.slicer.org/t/support-for-pathology-dicom/42248/1 "2025-03-21T16:22:39Z")

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I tried loading some DICOM microscopy images from [IDC](https://zenodo.org/records/12689994), but Slicer does not open them properly. [HistomicsTK](https://github.com/DigitalSlideArchive/digital_slide_archive/) does open some of them (bigger files). Is this the format [mentioned](https://discourse.slicer.org/t/fail-to-load-a-big-tiff-stack/4832/8) long ago by @pieper? Am I missing some Slicer extension? Does @fedorov have some advice?

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**Author:** ![fedorov](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/fedorov/32/14_2.png) [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Post date:** [March 21, 2025, 5:04pm UTC](https://discourse.slicer.org/t/support-for-pathology-dicom/42248/2 "2025-03-21T17:04:10Z")

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> [@dzenanz](#):
>
> but Slicer does not open them properly

I am not surprised by this. I’ve seen some demos in the past, but I am not sure how robust or maintained those are, if still available in some extensions.

> [@dzenanz](#):
>
> [HistomicsTK](https://github.com/DigitalSlideArchive/digital_slide_archive/) does open some of them (bigger files).

Can you give more details? Can you share pointers to the samples from IDC that open and do not open in HistomicsTK? Any errors? Ideally, it would be great to continue IDC-related discussions in the [IDC forum](https://discourse.canceridc.dev/).

> [@dzenanz](#):
>
> Is this the format [mentioned](https://discourse.slicer.org/t/fail-to-load-a-big-tiff-stack/4832/8) long ago by @pieper?

IDC digital pathology images are stored as DICOM Whole Slide Imaging (WSI) objects. All of those images in IDC right now are [dual personality DICOM-TIFF](https://learn.canceridc.dev/dicom/dicom-tiff-dual-personality-files), which means that each file can be loaded by either DICOM or TIFF reader. A caveat is that DICOM represents each layer of the pyramid as a separate instance/file, so it is not a 1-to-1 mapping to the original TIFF that contains the entire pyramid in a single file. Overall, I encourage ignoring the TIFF part and work with those files as just DICOM WSI.

At this point, DICOM WSI is supported natively by several open source tools, including [OpenSlide](https://openslide.org/formats/dicom/), BioFormats [bfconvert](https://bio-formats.readthedocs.io/en/stable/users/comlinetools/conversion.html) and [wsidicom](https://github.com/imi-bigpicture/wsidicom). I would be very surprised if none of those libraries is already in use by HistomicsTK, so perhaps it would not be a big effort to fix this.

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**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [March 21, 2025, 5:16pm UTC](https://discourse.slicer.org/t/support-for-pathology-dicom/42248/3 "2025-03-21T17:16:24Z")

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@dzenanz what operations did you have in mind?

You may want to look at SlicerBigImage:

> **[GitHub - gaoyi/SlicerBigImage: Large (GB and above) scale microscopic image...](https://github.com/gaoyi/SlicerBigImage)**
>
> Large (GB and above) scale microscopic image computing using 3D Slicer

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**Author:** ![dzenanz](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/dzenanz/32/1992_2.png) [@dzenanz](https://discourse.slicer.org/u/dzenanz)\
**Post date:** [March 21, 2025, 6:33pm UTC](https://discourse.slicer.org/t/support-for-pathology-dicom/42248/4 "2025-03-21T18:33:24Z")

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I have BigImage extension you pointed out Steve, but it did not help.

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**Author:** ![dzenanz](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/dzenanz/32/1992_2.png) [@dzenanz](https://discourse.slicer.org/u/dzenanz)\
**Post date:** [March 21, 2025, 6:42pm UTC](https://discourse.slicer.org/t/support-for-pathology-dicom/42248/5 "2025-03-21T18:42:40Z")

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Thanks for a detailed response Andrey. I was unaware they are dual DICOM/TIFF images. But renaming `M:\Dev\PSI\IDC\ccdi_mci\PBBHMD\2.25.89245761488191018377338178437808212829\SM_1.3.6.1.4.1.5962.99.1.852650165.48323970.1727429535925.4.0\21a0550d-a2ad-4345-9838-7be3d226a093.dcm` (part of [CCDI-MCI](https://zenodo.org/records/14009669)) into .tif and drag/dropping into Slicer results in the same problematic wrong size/layout as when loading as DICOM:

 ![Screenshot 2025-03-21 14.38.30](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/c/6/c6b068314e40a7d11d76a831cfddaf84cfc6b54a.jpeg)

I will follow-up with HistomicsTK-related post in IDC forum.

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**Author:** ![fedorov](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/fedorov/32/14_2.png) [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Post date:** [March 21, 2025, 6:56pm UTC](https://discourse.slicer.org/t/support-for-pathology-dicom/42248/6 "2025-03-21T18:56:46Z")

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If you just want to load images, it should work with the free open source QuPath [https://qupath.github.io/](https://qupath.github.io/), which wraps both of the aforementioned OpenSlide and Bioformats libraries, and can read DICOM WSI natively.

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**Author:** ![curtislisle](https://avatars.discourse-cdn.com/v4/letter/c/48db29/32.png) [@curtislisle](https://discourse.slicer.org/u/curtislisle)\
**Post date:** [March 21, 2025, 6:59pm UTC](https://discourse.slicer.org/t/support-for-pathology-dicom/42248/7 "2025-03-21T18:59:50Z")

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These microscopy and whole slide images from IDC are DICOM-WSI, not the radiology type of DICOM that ITK is expecting. These images need a library like openslide or wsi-dicom OR kitware’s large-image to read them and write out a selected resolution as a traditional TIFF for reading by ITK. They are basically multi-resolution TIFFs.

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**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [March 21, 2025, 7:34pm UTC](https://discourse.slicer.org/t/support-for-pathology-dicom/42248/8 "2025-03-21T19:34:56Z")

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@dzenanz you still haven’t described what exactly you are trying to accomplish.

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**Author:** ![dzenanz](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/dzenanz/32/1992_2.png) [@dzenanz](https://discourse.slicer.org/u/dzenanz)\
**Post date:** [March 21, 2025, 7:48pm UTC](https://discourse.slicer.org/t/support-for-pathology-dicom/42248/9 "2025-03-21T19:48:14Z")

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I am trying to view IDC microscopy images quickly and conveniently, preferably without installing much additional software.

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**Author:** ![dzenanz](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/dzenanz/32/1992_2.png) [@dzenanz](https://discourse.slicer.org/u/dzenanz)\
**Post date:** [March 21, 2025, 8:40pm UTC](https://discourse.slicer.org/t/support-for-pathology-dicom/42248/10 "2025-03-21T20:40:18Z")

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I realized that the DICOM images HistomicsTK cannot open are the regular (radiology) ones, which Slicer can open.

The ultimate goal I was pursuing was finding paired stained/unstained microscopy images (ideally with segmented cancer cells, or with a stain which highlights the cancer cells). The follow-up IDC forum question is [here](https://discourse.canceridc.dev/t/unstained-and-paired-microscopy-images/705).

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<div class="post-metadata">

**Author:** ![dzenanz](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/dzenanz/32/1992_2.png) [@dzenanz](https://discourse.slicer.org/u/dzenanz)\
**Post date:** [March 25, 2025, 4:00pm UTC](https://discourse.slicer.org/t/support-for-pathology-dicom/42248/11 "2025-03-25T16:00:44Z")

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I see a path forward. ITK remote module [IOOpenSlide](https://github.com/InsightSoftwareConsortium/ITKIOOpenSlide) allows use of OpenSlide, [latest (4.0) release](https://github.com/openslide/openslide/releases/tag/v4.0.0) of which supports DICOM-WSI standard. Their binary Windows distribution has a DLL, so work will be needed to integrate this. But there is hope. Most tests pass:

```log
1>67% tests passed, 3 tests failed out of 9
1>
1>Label Time Summary:
1>IOOpenSlide = 32.35 sec*proc (9 tests)
1>
1>Total Test time (real) = 32.36 sec
1>
1>The following tests FAILED:
1> 3 - itkOpenSlideTestMetaData (Failed) IOOpenSlide
1> 8 - itkOpenSlideTestApproximateStreaming (Failed) IOOpenSlide
1> 9 - itkOpenSlideTestStreaming (Failed) IOOpenSlide

```

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<div class="post-metadata">

**Author:** ![dzenanz](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/dzenanz/32/1992_2.png) [@dzenanz](https://discourse.slicer.org/u/dzenanz)\
**Post date:** [March 26, 2025, 6:44pm UTC](https://discourse.slicer.org/t/support-for-pathology-dicom/42248/12 "2025-03-26T18:44:40Z")

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Good news: the test failures are due to using a different version of OpenSlide library.