First post here! I’ve searched around and can’t find anything on this so here goes.
About the dataset:
-Micro CT analysis images of mouse hind limb counterstained with a staining agent to image soft and hard tissue
-80 image stacks of 445 images per stack.
-Attached are 4 example images from a stack with the first (153) and last (597) images from the stack and two images in the middle. (First is attached, the rest is on dropbox via link (may take a bit to upload if you’re quick on the response): https://www.dropbox.com/sh/rj0q15lqsm1dqgc/AACKVvs8Ce-8YxpYMNFvFexka?dl=0)
About the analysis:
We wish to measure the amount/volume of soft tissue in the image stack, and hopefully (due to the stain having 100% penetrance) derive some information about muscle quality from stain intensity. We then wish to analyse the bone, likely using BoneJ or analyzepro
About the problem:
The counterstain has worked too well! Upon attempt of analysis, I can’t find a reliable way (aside from roi selection of every image by hand which is not feasible… 80*445) to seperate out soft from bone tissue. I have tried thresholding on a number of programs inc. AnalyzePro and Fiji but to know avail. Tech support from Analyze pro say it can’t be done via thresholding.
Is there a way to select an ROI by hand say every 50 slices and have ImageJ/FIJI automatically join up the ROI’s?
If so, does BoneJ allow this method for analysis within its parameters?
If not, any ideas?
Thank you in advance to anyone that is willing to assist!
V112M1__IR_rec00000153.bmp (5.7 MB)