I am using the Cavalieri estimator to estimate area and volume of different brain regions in a slide. However I have some slides with artifacts in one of the regions while the other ones are useful. I am aware that I can account for a missing sections using the “Account for Missing Section” probe, but is there a way to account just for missing regions in a slide?
Thank you for your question. This is a topic where we have to be careful since we are compensating for data that is not available. What we should think about is how many sections are we using for the volume estimation and how many are missing. Let’s say you want to estimate the volume of a 3-D anatomical region, call it region X. And let’s say that there are 120 forty micron thick sections that make up region X. We won’t look at all of them of course, we’ll use an interval, and I’ll choose that interval so it gives me about ten sections. The section interval will be twelve, and twelve goes into 120, ten times. The interval is twelve, and you pick a random number between one and twelve and those will be your sections, let’s say the random number is eight. Now you know you will be looking at sections 8, 20, 32, 44, 56, 68, 80, 92, and 104 (nine sections due to the random start being eight). Your question I think is, what if for instance, section 32 is ripped or missing.
The first thing you could try is determining another random start. If you can do this and all the sections are available, then that is the way to go. The second thing to try is look for section 31 or 33, it is OK to substitute in an adjacent section now and then; it is probably not worth humanely killing another animal when you can just substitute in a neighboring section; a little jitter in the section interval will probably not hurt. If neither of these ideas work, you can consider taking the mean of all the other sections and substituting that in (that is what the ‘account for missing sections’ function does in SI) or you could consider taking the mean of the two adjacent sections and using that for the missing
section. But only substitute in the mean from the adjacent sections in very rare occasions when it makes sense. For example if half the sections are missing you would never consider taking the means of the sections that are not missing and using that. You would only consider this maybe for one section.