Question
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.

Similar questions and discussions

Does anybody know how we can download a video from www.jove.com?
Question
29 answers
  • Vahid AlimardaniVahid Alimardani
Dear friends,
I can download pdf of articles from www.jove.com, but i need video. Is there any especial way or replace website to download their video like you tube converter for you tube?
thanks a lot
Scientists Support Ukraine
Discussion
Be the first to reply
  • Ijad MadischIjad Madisch
Like so many, I am shocked and saddened at seeing war break out in Europe. My thoughts – and those of the ResearchGate team – are with the people of Ukraine and everyone affected.
ResearchGate is an international company, whose purpose is to enable scientists across the world to work together openly and collaboratively, regardless of borders or nationality. We have people from over 40 countries on our staff of around 200, and being based in Berlin, we are profoundly aware of the human cost of conflicts, the echoes of which have shaped and scarred our home city. We join with the international community in condemning the actions of the Russian state.
We have been asking ourselves: What can we do?
From today, we will offer free advertising space worth $2.5 million on our network to humanitarian organizations working to respond to the crisis. ResearchGate benefits from over 50 million visitors every month, and we hope this initiative can help raise funds and awareness for those organizations that are having direct impact and need support.
We also want to use our platform to highlight the response from the scientific community. Personally, I have found the messages of support from scientists everywhere to be truly heartfelt, and I would like to highlight some of the community initiatives I’ve seen here:
Additionally, I’m posting here some of the organizations responding to the crisis and actively soliciting donations:
To help gather more support for these initiatives, please consider sharing this post further (you don’t need a ResearchGate account to see it), and I will continue to update it with other initiatives as I find them. You can also click “Recommend” below to help others in your ResearchGate network see it. And if you know of any other community initiatives that we can share here please let us know via this form: https://forms.gle/e37EHouWXFLyhYE8A
-Ijad Madisch, CEO & Co-Founder of ResearchGate
-----
Update 03/07:
This list outlines country-level initiatives from various academic institutions and research organizations, with a focus on programs and sponsorship for Ukrainian researchers:
As Publons has been merged into Clarivate. Then, how peer review records can be added to author profile?
Discussion
3 replies
  • Hasanain OdharHasanain Odhar
Previously, I forward peer review credit email to reviews@publons.com to obtain the review record in my profile in Publons. But now after Publons has been merged into clarivate, this method seems not working anymore. Any suggestions or ideas in this regard?

Related Publications

Article
Full-text available
Background Imaging techniques used to measure hippocampal atrophy are key to understanding the clinical progression of Alzheimer's disease (AD). Various semi-automated hippocampal segmentation techniques are available and require human expert input to learn how to accurately segment new data. Our goal was to compare 1) the performance of our automa...
Got a technical question?
Get high-quality answers from experts.