AFM image analysis

Dear Colleagues,

I am new to this forum and would like to find some help regarding the analysis of the following type of images.

The image below is of skin at high resolution using AFM. I would to be able to quantify the % of the image showing aligned fibrils vs non-aligned fibrils. I was wondering if you may be able to advise me on how to proceed.

I have very limited knowledge in image post-processing - so any step-by-step input would be greatly appreciated.

Thanks
Laurent
test

@L.Bozec

I would point you to two tools coming from our group: CT-FIRE and CurveAlign (depending on what exactly you want to measure and how). Those are ImageJ-independent tools… take a look and see if they’d do the trick.

For ImageJ tools… you can search on the ImageJ wiki. There is a plugin called Directionality that might work for you. And there is OrientationJ out of BIG-EPFL.

Take a look at those tools - give one or more a try… and if you have specific questions there-after - post again! We are here to help.

eta :slight_smile:

Good day Laurent,

from a pre-processed version (windowed and DC-free, i.e. the shown image was actually bipolar and the mean gray corresponds to zero) of your sample image
skinAFM
I generated what I call its “Orientation Salience”-function:

It shows the salience of image structures as a function of the orientation angle. The plot starts with the horizontal orientation and the angle increases counter-clockwise. Please note that the salience depends also on the contrast of the structures, i.e. it isn’t a purely geometric measure!

I have very limited knowledge in image post-processing - so any step-by-step input would be greatly appreciated.

This report describes the generation of “Orientation Salience”-functions and you may probably realize that this is not the way you like to go …

So if you think that this kind of analysis is helpful for you and if you have only a limited amout of images to analyze, you could make them accessible for me in the original uncompressed RAW- or TIF-format and I’d return the plots to you.

Regards

Herbie