# Analysis of plant stem, roots and froots

**URL:** <https://discourse.slicer.org/t/analysis-of-plant-stem-roots-and-froots/17999>\
**Category:** Support\
**Created:** [June 7, 2021, 4:47pm UTC](https://discourse.slicer.org/t/analysis-of-plant-stem-roots-and-froots/17999 "2021-06-07T16:47:03Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![sreenivasalluri](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/sreenivasalluri/32/11171_2.png) [@sreenivasalluri](https://discourse.slicer.org/u/sreenivasalluri)\
**Post date:** [June 7, 2021, 4:47pm UTC](https://discourse.slicer.org/t/analysis-of-plant-stem-roots-and-froots/17999/1 "2021-06-07T16:47:03Z")

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Can we analyze the plant roots and stems and fruits?  
Dr. Sreenivas Alluri

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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 7, 2021, 5:58pm UTC](https://discourse.slicer.org/t/analysis-of-plant-stem-roots-and-froots/17999/2 "2021-06-07T17:58:49Z")

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Yes, people have done this before and reported good results (you might be able to find some publications on this). If you have good scans then a lot of the same tools should work, like segmentation, vessel analysis, etc.

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**Author:** ![sreenivasalluri](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/sreenivasalluri/32/11171_2.png) [@sreenivasalluri](https://discourse.slicer.org/u/sreenivasalluri)\
**Post date:** [June 8, 2021, 2:56am UTC](https://discourse.slicer.org/t/analysis-of-plant-stem-roots-and-froots/17999/3 "2021-06-08T02:56:04Z")

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Thankyou  
Can you provide any journal papers for reference.  
Thankyou

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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 8, 2021, 5:21pm UTC](https://discourse.slicer.org/t/analysis-of-plant-stem-roots-and-froots/17999/4 "2021-06-08T17:21:14Z")

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With [this google search](https://www.google.com/search?q=3d+%22slicer%22+plant+roots&sxsrf=ALeKk02c-Iymaz7u9NfEq36UaOaypCT5Rw%3A1623172638740&ei=Hqa_YOPLLJKDtQaKwLOYBg&oq=3d+%22slicer%22+plant+roots&gs_lcp=Cgdnd3Mtd2l6EAMyBAgjECc6BwgjELADECc6BwgAEEcQsANQuUZYqFhgoltoAXACeACAAfMCiAHaBJIBBzAuMi4wLjGYAQCgAQGqAQdnd3Mtd2l6yAEJwAEB&sclient=gws-wiz&ved=0ahUKEwjj0qmkxYjxAhWSQc0KHQrgDGMQ4dUDCA4&uact=5) I found some good hits:

> [@Support for .AIM/.isq files generated on Scanco microCT](https://discourse.slicer.org/t/support-for-aim-isq-files-generated-on-scanco-microct/6261):
>
> I might be the odd one out here working on plants. I am new to Slicer and trying to use Scanco microCT 50 for scanning my plant root samples. Would like to know if you are planning to give support for direct import of .AIM/other formats that Scanco imagers generate.

[https://www.slicer.org/wiki/Main\_Page/SlicerCommunity/2019#Isolating\_Phyllotactic\_Patterns\_Embedded\_in\_the\_Secondary\_Growth\_of\_Sweet\_Cherry\_.28Prunus\_Avium\_L..29\_Using\_Magnetic\_Resonance\_Imaging](https://www.slicer.org/wiki/Main_Page/SlicerCommunity/2019#Isolating_Phyllotactic_Patterns_Embedded_in_the_Secondary_Growth_of_Sweet_Cherry_.28Prunus_Avium_L..29_Using_Magnetic_Resonance_Imaging)