Root phenotyping: measuring roots with ImageJ SmartRoot plugin

PS: You need to pay attention to the scale function to correspond the pixels to the centimeters.
I tried to make this little tutorial to present an interesting plugin when you want to measure secondary or tertiary roots in addition to the primary. The data analysis is easy afterwards with the CSV file.
If there is a correction to make, put it in comment, thank you.
Lobet G, Pages L, Draye X (2011) A Novel Image Analysis Toolbox
Enabling Quantitative Analyses of Root System Architecture
Plant Physiology, Vol. 157, pp 29-39
#imagej #fiji #plugin #smartroot #phenotyping #phenotypage #racine #root #roots
Music: audiohub.com/song/right-away

[@dr.muhammadsameeullah9400]

Excellent. you are lifesaver.

[@pallavisingh8898]

Good explanation

[@NguyenDaoNgocMinh]

Hi. Your video is life-saving to me. But I have a problem. About the child density, I don't understand how Smartroot can calculate this parameter. Could you help me with this? I really want to know. Many thanks.

[@CheFaire]

Hi, I think that if you set the scale, the software will estimate the number of roots per cm of primary root through the position (in pixels ?) of the lateral root as long as the laterals are associated to the primary root and this, for each plant, but I haven't developed the software so I'm not sure

[@nathaliedelherbe6223]

Hi, great video!, by any chance do you know how to make the SmartRoot Explorer window to recognize folders/files on my MacBook?, I installed the plugins, and the program opens, however I can't open any file since the Explorer window appears empty. Thanks!

[@CheFaire]

Hi thank you. I had the same problem. To solve this problem, I had to authorize Image J to access to the files/folder. When I updated my Mac, it asked me automatically. Otherwise, you can modify some settings : Choose Apple menu > System Settings, then click Privacy & Security in the sidebar. Click Files and Folders. For each app (here Image J/ Fiji) in the list, turn the ability to access files and folders in specific locations on or off. Hope it'll help.

[@niarsimerryhemelda3815]

Hi, great tutorial! Many thanks. Btw, I have a problem. So far, I managed to install the smartRoot plugin in my imageJ. I opened the SmartRoot window and followed your steps until inverting the image. However, it couldn't trace the root. I even used the root image provided by the SmartRoot quick start folder. Even though I clicked option + left click. Just no response. I couldn't see any nodes or axis on the image. Do you have any idea? Thanks in advance.

[@CheFaire]

Hi, thank you for your comment. What is written on the "Log" window when you try to trace a root ?

[@dr.muhammadsameeullah9400]

I have a question. Is it needed to set scale before measurements? If so, setting scale is same way as in ImageJ while using SmartRoot? Thanks

[@CheFaire]

Honestly, I think this is important. You can do it with the SmartRoot window in "settings" by checking the box for pixels/cm. First, the ideal is to take the picture of your petri dishes with a ruler next to them (or you use the petri dish as your reference). Then, you use the straight line tool, you trace a line on the ruler for 1 cm on your picture (or the petri dish from one side the other), you go back to the settings, you click "get line", it will give you the number of pixels for 1cm (or the length of your petri dish). Then, you're supposed to have all the measurements in cm which is easier for the analysis later.

[@athiyaunding7353]

hello! I dont understand why the apps doesnt trace the roots even after checking both axis and nodes as well as doing the alt + left click. hope u see this soon, thank you!

[@CheFaire]

Have you inverted the colors like shown on the video ? Moreover, what information do you have on the "Log" window when you click on the picture ?

[@athiyaunding7353]

@@CheFaire I think i got the problem. The image was directly dragged onto the ImageJ ribbon. I opened it from the smartroot explorer then it worked. Thank you for this. May i ask if this is accurate?

[@josephzvomuya2934]

Hi @chefaire can i contact you for a one on one tutorial im having problem tracing my roots