# MEMOS: New extension for deep-learning based segmentation of 3D fetal mice scans.

**URL:** <https://discourse.slicer.org/t/memos-new-extension-for-deep-learning-based-segmentation-of-3d-fetal-mice-scans/27956>\
**Category:** Announcements\
**Created:** [February 21, 2023, 6:15pm UTC](https://discourse.slicer.org/t/memos-new-extension-for-deep-learning-based-segmentation-of-3d-fetal-mice-scans/27956 "2023-02-21T18:15:56Z")\
**Posts on this page:** 9\
**Page:** 1

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**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [February 21, 2023, 6:15pm UTC](https://discourse.slicer.org/t/memos-new-extension-for-deep-learning-based-segmentation-of-3d-fetal-mice-scans/27956/1 "2023-02-21T18:15:56Z")

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We would like to announce a new Slicer extension, [MEMOS](https://github.com/SlicerMorph/SlicerMEMOS), for deep-learning based segmentation of diceCT scans of fetal mice. See the repository for quick installation instructions.

Accompanying paper can be found in Biology Open: [Deep learning enabled multi-organ segmentation of mouse embryos | Biology Open | The Company of Biologists](https://journals.biologists.com/bio/article/12/2/bio059698/287076/Deep-learning-enabled-multi-organ-segmentation-of)

Using GPU, MEMOs provide segmentation of 50 anatomical structures in the [E15.5 atlas provided by the International Mouse Phenotyping Consortium](http://www.mouseimaging.ca/technologies/mouse_atlas/mouse_embryo_atlas.html) in about 40-60 seconds.

In future, we plan to incorporate more developmental time points as a separate trained networks.

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/e/7/e7ebd5113bbda1cd7c1646f1fb157bac72fe914d.jpeg)

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**Author:** ![Mate\_Toth](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/mate_toth/32/4316_2.png) [@Mate\_Toth](https://discourse.slicer.org/u/Mate_Toth)\
**Post date:** [February 23, 2023, 1:36pm UTC](https://discourse.slicer.org/t/memos-new-extension-for-deep-learning-based-segmentation-of-3d-fetal-mice-scans/27956/2 "2023-02-23T13:36:03Z")

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Hi, that sounds great, I’d like to try it, but I’m unable to install this extension  
 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/d/d/ddbb4b376355e4a2b99d18276d4dd81055c5f91c.png)

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**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [February 23, 2023, 4:08pm UTC](https://discourse.slicer.org/t/memos-new-extension-for-deep-learning-based-segmentation-of-3d-fetal-mice-scans/27956/3 "2023-02-23T16:08:55Z")

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Which os do you use?

That might be related with the patch release last night. I just downloaded and install fresh on windows (v5.2.2), can you try again?

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**Author:** ![Mate\_Toth](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/mate_toth/32/4316_2.png) [@Mate\_Toth](https://discourse.slicer.org/u/Mate_Toth)\
**Post date:** [February 23, 2023, 4:44pm UTC](https://discourse.slicer.org/t/memos-new-extension-for-deep-learning-based-segmentation-of-3d-fetal-mice-scans/27956/4 "2023-02-23T16:44:18Z")

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I’m using WIN10 and slicer 5.2.1 r31317 / 77da381, still not working, I’ll update to 5.2.2 and try again. Thank you

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**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [February 23, 2023, 4:56pm UTC](https://discourse.slicer.org/t/memos-new-extension-for-deep-learning-based-segmentation-of-3d-fetal-mice-scans/27956/5 "2023-02-23T16:56:29Z")

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İ see. As it is a new extension, it is only available for stable or 5.3.0 (or higher) previews.  
Yes, try with latest stable.

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**Author:** ![Jan\_Lennart](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jan_lennart/32/15701_2.png) [@Jan\_Lennart](https://discourse.slicer.org/u/Jan_Lennart)\
**Post date:** [February 24, 2023, 2:39pm UTC](https://discourse.slicer.org/t/memos-new-extension-for-deep-learning-based-segmentation-of-3d-fetal-mice-scans/27956/6 "2023-02-24T14:39:20Z")

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I have only used Total Segmentator so far but MEMOS also looks fantastic.

Is there anything comparable available for adult mice? I have \>1000 CT scans of mice that need to be segmented (mainly liver, kidneys, and heart).

Best, Jan

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**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [February 24, 2023, 3:17pm UTC](https://discourse.slicer.org/t/memos-new-extension-for-deep-learning-based-segmentation-of-3d-fetal-mice-scans/27956/7 "2023-02-24T15:17:08Z")

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No, we don’t have anything for adult mice. We don’t really do physiology, mostly development.

However, it is getting easier to train deep learning networks for custom segmentation tasks. So if you have already manually segmented ones that can be used as training data, it might be just a matter of putting some GPUs to use.

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [February 11, 2024, 12:09pm UTC](https://discourse.slicer.org/t/memos-new-extension-for-deep-learning-based-segmentation-of-3d-fetal-mice-scans/27956/8 "2024-02-11T12:09:14Z")

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12 posts were split to a new topic: [AI segmentation of bird brain](https://discourse.slicer.org/t/ai-segmentation-of-bird-brain/34246)

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [February 21, 2024, 8:33pm UTC](https://discourse.slicer.org/t/memos-new-extension-for-deep-learning-based-segmentation-of-3d-fetal-mice-scans/27956/20 "2024-02-21T20:33:20Z")

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15 posts were split to a new topic: [Problem using MEMOS extension](https://discourse.slicer.org/t/problem-using-memos-extension/34456)