# \#microscopy

**URL:** https://discourse.slicer.org/tag/microscopy/32.md

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## [New extension: OMEZarr - open OME-Zarr images directly in Slicer](https://discourse.slicer.org/t/new-extension-omezarr-open-ome-zarr-images-directly-in-slicer/48238)

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**Author:** [@vboussot](https://discourse.slicer.org/u/vboussot)\
**Replies:** 6\
**Last updated:** [October 2, 2026, 5:55pm UTC](https://discourse.slicer.org/t/new-extension-omezarr-open-ome-zarr-images-directly-in-slicer/48238 "2026-10-02T17:55:21Z")

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Hi all, We’re happy to announce OMEZarr, a new extension from Fideus Labs that opens and saves OME-Zarr images. It is available in the Extensions Manager for Slicer 5.12.4 and the Preview release, on Linux, macOS and Wi…

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## [Support for pathology DICOM](https://discourse.slicer.org/t/support-for-pathology-dicom/42248)

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**Author:** [@dzenanz](https://discourse.slicer.org/u/dzenanz)\
**Replies:** 11\
**Last updated:** [March 26, 2025, 6:44pm UTC](https://discourse.slicer.org/t/support-for-pathology-dicom/42248 "2025-03-26T18:44:40Z")

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I tried loading some DICOM microscopy images from IDC, but Slicer does not open them properly. HistomicsTK does open some of them (bigger files). Is this the format mentioned long ago by @pieper? Am I missing some Slicer…

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## [3D image registration of microscopy image](https://discourse.slicer.org/t/3d-image-registration-of-microscopy-image/33604)

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**Author:** [@ylcnkzy](https://discourse.slicer.org/u/ylcnkzy)\
**Replies:** 2\
**Last updated:** [January 10, 2024, 3:16pm UTC](https://discourse.slicer.org/t/3d-image-registration-of-microscopy-image/33604 "2024-01-10T15:16:24Z")

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Hi Everyone, I have 2 different microscopy images in 3D tiff format. Now, both images cover similar areas and structures (image below). I plan to align and register them, and create a deformation vector field) for t…

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## [3D registration of 3D microscopy images](https://discourse.slicer.org/t/3d-registration-of-3d-microscopy-images/32204)

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**Author:** [@ylcnkzy](https://discourse.slicer.org/u/ylcnkzy)\
**Replies:** 3\
**Last updated:** [November 5, 2023, 6:13pm UTC](https://discourse.slicer.org/t/3d-registration-of-3d-microscopy-images/32204 "2023-11-05T18:13:46Z")

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Greetings Everyone, In our lab, we have developed a methodology that allows us to stain the same sample for different biological targets at different time points, and enable us to visualize the same sample again and aga…

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## [What would be the best way to let a user select scenes and channel colours in a microscopy oriented importer?](https://discourse.slicer.org/t/what-would-be-the-best-way-to-let-a-user-select-scenes-and-channel-colours-in-a-microscopy-oriented-importer/31595)

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**Author:** [@EgorZindy](https://discourse.slicer.org/u/EgorZindy)\
**Replies:** 5\
**Last updated:** [September 6, 2023, 9:01pm UTC](https://discourse.slicer.org/t/what-would-be-the-best-way-to-let-a-user-select-scenes-and-channel-colours-in-a-microscopy-oriented-importer/31595 "2023-09-06T21:01:47Z")

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Hello everyone. So for my CZI importer, there are two things I think need to be user-selectable at import time: A CZI file may contain multiple scenes, and a user may decide which scenes need importing. The channel co…

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## [Working on a CZI Zeiss microscopy image stack reader for 3D slicer, any help or advice welcome](https://discourse.slicer.org/t/working-on-a-czi-zeiss-microscopy-image-stack-reader-for-3d-slicer-any-help-or-advice-welcome/30769)

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**Author:** [@EgorZindy](https://discourse.slicer.org/u/EgorZindy)\
**Replies:** 11\
**Last updated:** [August 24, 2023, 10:15am UTC](https://discourse.slicer.org/t/working-on-a-czi-zeiss-microscopy-image-stack-reader-for-3d-slicer-any-help-or-advice-welcome/30769 "2023-08-24T10:15:54Z")

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Some general info: Operating system: Windows 10 Slicer version: 5.3.0 - 2023.06.17 Expected behavior: 3D stack(s) imported from a CZI scene with minimum hassle for the user… Actual behavior: Work in progress, 3D view …

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## [Segmentations can get big!](https://discourse.slicer.org/t/segmentations-can-get-big/545)

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**Author:** [@Fernando](https://discourse.slicer.org/u/Fernando)\
**Replies:** 12\
**Last updated:** [October 23, 2019, 4:36pm UTC](https://discourse.slicer.org/t/segmentations-can-get-big/545 "2019-10-23T16:36:04Z")

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Hi all (specially @lassoan and @cpinter), I am working with a 2D segmentation. After saving it, I use Python to process the NRRD files. The size of my master volume node is 28320 x 15232, it's a scanned histological sl…