# ABC Atlas: MERFISH cell segmentation in 3D

**URL:** <https://community.brain-map.org/t/abc-atlas-merfish-cell-segmentation-in-3d/3955>\
**Category:** Allen Brain Cell (ABC) Atlas\
**Created:** [December 9, 2024, 3:05pm UTC](https://community.brain-map.org/t/abc-atlas-merfish-cell-segmentation-in-3d/3955 "2024-12-09T15:05:23Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![simonf](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/simonf/32/2058_2.png) [@simonf](https://community.brain-map.org/u/simonf)\
**Post date:** [December 9, 2024, 3:05pm UTC](https://community.brain-map.org/t/abc-atlas-merfish-cell-segmentation-in-3d/3955/1 "2024-12-09T15:05:23Z")

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Hi,

In the ABC Atlas webinar ( **[https://www.youtube.com/watch?v=fuqpSZp7uk0](https://www.youtube.com/watch?v=fuqpSZp7uk0)**) you mentioned that each MERFISH z plane was segmented separately and then combined. How did you match cells when combining? Based on the distance of the cell centroid?

Much appreciated!  
Simon

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**Author:** ![simonf](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/simonf/32/2058_2.png) [@simonf](https://community.brain-map.org/u/simonf)\
**Post date:** [December 9, 2024, 3:06pm UTC](https://community.brain-map.org/t/abc-atlas-merfish-cell-segmentation-in-3d/3955/2 "2024-12-09T15:06:47Z")

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@mkunst23

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**Author:** ![mkunst23](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/mkunst23/32/320_2.png) [@mkunst23](https://community.brain-map.org/u/mkunst23)\
**Post date:** [January 29, 2025, 4:29am UTC](https://community.brain-map.org/t/abc-atlas-merfish-cell-segmentation-in-3d/3955/3 "2025-01-29T04:29:53Z")

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Sorry for the late reply. I also must have misspoken. The z-planes were segmented each segmented separately, they were segmented with all z-planes at once in 3D.

Hope that helps,  
Michael

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**Author:** ![simonf](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/simonf/32/2058_2.png) [@simonf](https://community.brain-map.org/u/simonf)\
**Post date:** [January 29, 2025, 9:58am UTC](https://community.brain-map.org/t/abc-atlas-merfish-cell-segmentation-in-3d/3955/4 "2025-01-29T09:58:08Z")

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That makes sense, thank you.