Finding contours of a plant root

I have an image which has roots like this:  I want to crop each root individually out. I initially thought of heavy dilation followed by erosion and contour detection of the blob, but since the roots are thin, it does not work well. I also directly applied canny edge and contour detection like this image below. It has around 62000 contours, but I cannot use it to get the outline of each root as all are fragments.  Can anyone suggest me a better approach to tackle this problem! Thanks