# Segment middle & inner ear

**URL:** <https://discourse.slicer.org/t/segment-middle-inner-ear/43447>\
**Category:** Support\
**Tags:** segmentation, extensions-manager, dicom\
**Created:** [June 21, 2025, 3:13pm UTC](https://discourse.slicer.org/t/segment-middle-inner-ear/43447 "2025-06-21T15:13:57Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![Nadine\_Nabil](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/nadine_nabil/32/79414_2.png) [@Nadine\_Nabil](https://discourse.slicer.org/u/Nadine_Nabil)\
**Post date:** [June 21, 2025, 3:13pm UTC](https://discourse.slicer.org/t/segment-middle-inner-ear/43447/1 "2025-06-21T15:13:57Z")

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Hi everyone,  
I’m trying to segment the middle and inner ear in high anatomical detail using 3D Slicer. I need to extract small structures like:

 ![Screenshot 2025-06-21 180648](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/8/7/87c489e35345fd8ea701529a180281974ee81636.png)

Any advice or workflows for segmenting these fine structures?  
Should I do it all manually, or is there a better way?

Appreciate any tips or resources!

Thanks,  
Nadine

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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:** [June 21, 2025, 4:53pm UTC](https://discourse.slicer.org/t/segment-middle-inner-ear/43447/2 "2025-06-21T16:53:33Z")

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Do you mean from this image or from a CT? Assuming you mean CT, a lot depends on the resolution of the scan, but thresholding and scissors would be a place to start, but you could also try nnInteractive.

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**Author:** ![Nadine\_Nabil](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/nadine_nabil/32/79414_2.png) [@Nadine\_Nabil](https://discourse.slicer.org/u/Nadine_Nabil)\
**Post date:** [June 21, 2025, 5:00pm UTC](https://discourse.slicer.org/t/segment-middle-inner-ear/43447/3 "2025-06-21T17:00:10Z")

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Thank you for your reply!

I’m still quite new to Slicer. I’ve only worked on a 3D model of the sinus and nasal cavity, so I’m not yet familiar with all the available tools.

So far, I usually rely on thresholding, then do most of the refinement manually using Paint and Erase.

For this ear project, I’ll be working with CT data (not the endoscopic image), and I should be able to get high-resolution scans, but I’m not sure if there’s a specific tool that could make segmenting the tiny detailed parts (like the ones I highlighted in the pervious image ) easier — or if manual work is the only option.

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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:** [June 21, 2025, 5:04pm UTC](https://discourse.slicer.org/t/segment-middle-inner-ear/43447/4 "2025-06-21T17:04:19Z")

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There are lots of tutorials and videos so you can get an idea what worked for other people, but in the end you’ll need to experiment a bit. If you post data publicly along with your experiments other people may get inspired to give it a try and give you more concrete feedback.

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**Author:** ![Nadine\_Nabil](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/nadine_nabil/32/79414_2.png) [@Nadine\_Nabil](https://discourse.slicer.org/u/Nadine_Nabil)\
**Post date:** [June 21, 2025, 5:17pm UTC](https://discourse.slicer.org/t/segment-middle-inner-ear/43447/5 "2025-06-21T17:17:24Z")

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Thank you so much, Steve — I really appreciate your time and advice!

I understand that experimenting is key, and I’ll definitely do that.  
I just wanted to get a rough idea of how challenging this type of model might be, so I could estimate how much time it would take before diving in.

This project is a step up for me — so far, I’ve only worked on a 3D model of the sinus and nasal cavity — so I’m still learning and trying to plan accordingly.

Thanks again for your support!

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/f/b/fbb7d22f6213061d422a5eb32a09ccc64391fde2.jpeg)  
This is the first model I have made. I don’t know where my true level is.