Nanorod TEM segmentation/measurement




I am trying to find an automated method of measuring the aspect ratio of nanorods in a TEM image. It seems that the main problem is how close some of the particles are to each other. Any suggestions on which tools would be best for this? A sample image is attached:


Hi Andrew,

I suggest you threshold the image so you get a mask with white background and black nanorods, use the watershed tool to separate any close particles masked together and apply the analyze particles tool.

Watch out with the scale bar, however.

I hope that helps



Hi Fernando,

Thanks for the suggestion. Unfortunately, the watershed segmentation ends up dividing the nanorods into segments instead of separating touching particles.



Good day Andrew,

if possible try to disperse the particles until they don’t touch anymore and perhaps increase the spatial resolution of your images. Furthermore, try to avoid uneven ilumination and shades (positive or negative) that are present in your sample image.

Good image acquisition is key to satisfying image analysis. Post hoc processing can become quite costly and in most cases, will not generalize and will not lead to reasonable results.