Hi @ArneK, welcome to the forum!
The image you posted is very nice and since you have a significant number of them at such high resolution it must be a challenge to work with them in the ImageJ framework.
Have you checked out CLIJ2 and CLIJx plugins? These are great for X-ray tomography image sets since the plugin utilizes a dedicated or integrated graphics card to perform image processing steps. This speeds up these types of things very nicely if you need to use the ImageJ platform. Check out the website here https://clij.github.io/, the plugin is maintained by @haesleinhuepf and it has its own sub-category in the forum.image.sc here: https://forum.image.sc/tag/clij
I don’t have much experience with BoneJ and it may do exactly what you need it to. I did play around with your image a little bit in CLIJ2. Basically just performed a median smoothing of the slice, then Otsu’s thresholding, then a closing operation with a very high number of iterations (see the steps from ImageJ’s macro recorder below.
This result is close to what you have done with clicking points around some “edge”. I’m not sure how you decided on some of the points as there is no clear edge in the unprocessed slice so it’s either rather arbitrary or informed from your experience.
BTW, MorphoLib is a plugin that has some nice morphological operations (closing, opening, erosion, dilation, etc.) and I would suggest checking that out too.
Since your data sets are rather large, I suggest trying things out on a small subset of slices (10-20) first, then seeing if you can adapt things to your large image stack. There are plenty of examples of scripts on the CLIJ forum to help with setting things up in an ImageJ macro scripting language to get you started on that.
run("CLIJ2 Macro Extensions", "cl_device=[Quadro P3200]");
image1 = "40812984_fe_rec1327.tif";
image2 = "median1583229316";
radius_x = 3.0;
radius_y = 3.0;
Ext.CLIJ2_median2DSphere(image1, image2, radius_x, radius_y);
// threshold otsu
image3 = "threshold_otsu173268586";
image5 = "closing1324974869";
number_of_dilations_and_erotions = 175.0;
Ext.CLIJ2_closingDiamond(image3, image5, number_of_dilations_and_erotions);
Let me know if you have any questions, and good luck with your analyses!