I am looking for a fully automated program/application/plugin for analyzing G-ratios. I know of a couple of semi-automated plugins for ImageJ (http://gratio.efil.de/, http://cifweb.unil.ch/index.php?option=com_docman&task=cat_view&gid=18&Itemid=57), but the first one requires manual selection of each axon to be measured, and the second one requires manual selection of the inner and outer perimeters. This paper (http://link.springer.com/article/10.1007/s00371-011-0655-y) shows it can be done automatically within MATLAB. But I am hoping for a more user friendly method that doesn't require a specialized knowledge of MATLAB.
I've used this one http://gratio.efil.de/ to measure G-ratio's of rat phrenic and sciatic nerves. We had stained for lipids using a fluorescent green dye and gotten transverse images of the nerve using con-focal microscopy. Since we had such good contrast between the nerve (black) and the myelin (green) it was relatively simple to calculate g-ratios. The program is easy to use and you get quicker the amount of times you do it. I would say if you decide to use that one you need to make sure you have strong contrast and also to make sure you take the images at the highest resolution possible. We couldn't find any better way or more automated way to measure the G-ratios
There is not a perfect application. All fully automated programs are based in the contrast of the image that you take. When you prepare your samples for analyzing, myelin must be darker than axons. Then, the program can calculate G-ratios. However, some problems always appear. For example, two nerve fibers together are identified like one by the application. Other problem could be a lack of myelin staining that means application can not calculate G-ratios.
Other matter is what kind of nerve are you using. A large nerve, like sciatic nerve, is much easier than a small one. In addition, human nerves are better than rat ones because the size.
I've used this one http://gratio.efil.de/ to measure G-ratio's of rat phrenic and sciatic nerves. We had stained for lipids using a fluorescent green dye and gotten transverse images of the nerve using con-focal microscopy. Since we had such good contrast between the nerve (black) and the myelin (green) it was relatively simple to calculate g-ratios. The program is easy to use and you get quicker the amount of times you do it. I would say if you decide to use that one you need to make sure you have strong contrast and also to make sure you take the images at the highest resolution possible. We couldn't find any better way or more automated way to measure the G-ratios
We have calculated the rat G-ratio with Matlab code, we are still improving this code:
http://www.mathworks.com/matlabcentral/fileexchange/51025-measure-myelin-to-axon-diameter
Pls let us know your detail requirements, we will improve accordingly.
Hello Jun Steed Huang,
I'm trying to use this script to calculate the G ratio on EM pictures of mouse corpus callosum. But when I try to run my pictures it gives me an error in the imread line.
I don't know much about the MATLAB works, so I needed a little help to solve my problem.
Another question is if there is any way to have more information about each axon individually, i.e. diameter and G-ratio, and also the number of axons counted.
Thanks
If you have knowledge in Photoshop you can adjust the contrast between myelin staining and the axon and then to use the free software Image-J.
Has anyone had issues with the color of the cross placed at the random position in the image when using the http://gratio.efil.de/ application? Instead of red as stated in the usage documentation, it appears black and is difficult to see in the image. Any help is appreciated.
Andrew, we had a similar issue. To overcome, we used photoshop to convert the grayscale image into a RGB file. Then use this RGB file in imageJ. When you load gratio it will have a red crosshair.
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