Asked 8th Mar, 2022

Recommendations for segmentation software for 3D data MRI sets of plant roots?

Could anyone recommend a software that would help segment 3D MRI data sets of plant roots. I am currently working with ImageJ/Fuji and have played around with a number of the built in packages but haven't been able to produce the results I would like. Ideally I would like to extract information on root number, length, diameter and root volume in a (semi) automated way. Thanks in advance for any recommendations.

All Answers (3)

8th Mar, 2022
Marc W Van Iersel
University of Georgia
If you're willing to use Python, look into the OpenCV or PlantCV packages. There are some good YouTube videos on how to use them.
9th Mar, 2022
William Wheeler
Texas A&M University
Thanks Marc! I will look into this.
9th Mar, 2022
Marc W Van Iersel
University of Georgia
Sent me an email and I'll introduce you to someone at UGA who does a lot of 3d root system modelling.

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