(Suggestions/help)H&E Collagen fibre orientation or Polarisation microscopic image Collagen orientation

Hi all,

I have some tendon HE staining image and polarisation microscopic image for collagen bundle orientation analysis. Anyone has idea about it? I found it quiet different from cell orientation.

I have attached the images of both below.

Hope to hear from you soon,[18 WEEK Rabbit AUTO #1 40X.tif|attachment](uploa

d://eEomF4ytYZk2UMe3VxWi8mjIPfO.tif) (1.4 MB)

What exacly are you interested in?

Here is the result of a global orientation analysis of the central square region of the sample image taken from its green channel:

Here is the local indicator field taken from its green channel and superimposed to it:

Here is the histogram computed from the above indicator field:

Thanks so much for that! My aim is to quantify the waviness of the collagen bundle. I have upload another pic of tendon that looks quiet different from the previous one.


Frankly speaking, I 've no idea how you define

Of course orientation measures can give you a hint, i.e. they tell you to what degree structures deviate from a main direction but this is not a unique feature of “wavi” structures.

Here are the three displays for sample 2 (again the green channel):

When comparing the histograms of both samples please note the scale of the rel. frequency-axis [%]. (These histograms are density functions, i.e. their integrals are one.)

To discriminate between samples it may be sufficient to use the global “Orientation Salience Histograms”. I’m not familiar with this kind of data and I don’t know what’s important, so the decision is yours.
The analyses were done using this ImageJ-plugin. Plugins performing similarly are available from other download sites.

So many thanks! That is super helpful! I have used OrientationJ ImageJ plugin but it seems not really what I want. I tried the plugin you recommended it at least work so good on the global analysis for me!

Thanks again! I will update you with any further findings I get.


Hello there,
There is actually a plugin named “Waveness, Roughness” although I do not know if it comes with the install yet. If not you can get it on the plugins site and is quite straightforward and easy to use.
Good Luck,

This Waveness-Roughness-plugin performs a completely different kind of analysis and will be of no help with the data considered in this thread.

And you know this how ??? Let them decide.