Stereology on 2D MicroCT slices

Hi there,

Is it possible to do volume estimates on 2D images taken from a 3D MicroCT data set within stereo investigator desktop edition?

Hi there!

Thank you for your question. What file format are your images in? If SI-desktop can open them and you know the scaling, then you can certainly use SI-desktop to employ Cavalieri point-counting to estimate volumes.


Yes I can open the substack of images on SI-desktop but I am struggling with the Z scale correction factor because they are not traditional histology sections but are 2D trans-axial projections from the microCT scan. I am getting volume estimates that seem to be to small by a factor of 10 and I am wondering if the Z scale has something to do with this.


Hi Mary,

Because you are using MicroCT scans, you do not need to use the Correction Factor feature. Instead, select Focal Distance as the Distance Type for the Z scaling, and input the distance between focal planes (11 µm) in the Distance between images field. I expect this will produce more accurate volume estimates.

Hope this helps!

If the volume estimates you’re getting don’t seem right, it’s very likely that the scaling is incorrect.

A good check for the XY scaling is to use Trace>Measure Line and measure something of known size (like a cell or a hemisphere). If that is not correct, you need to change the X and Y scaling applied to images (11 in your screenshot above).

The Z scaling can be a bit trickier to get right, and checking it varies greatly from project to project. One of the best tests is to simply look at your image in the 3D window. If it looks “squished”, the Z scaling is probably not right. This can get a bit tricky to judge as certain tissue types, like Golgi stained neurons, tend to have a lot of “axial smear” and can look stretched even when they have the right Z scaling applied.

If you’re dealing with a Z stack where each plane is a section - for example, an image generated by NeuroInfo or BrainMaker - your distance between images number should be the section’s cut thickness * the section evaluation interval. As an example, if you took a 1 in 10 series (section 1, section 11, section 21…) at 5 microns cut thickness (block advance on the microtome), you would multiply 5 * 10 = 50. Pick focal distance (or physical distance / oil, which has a correction factor of 1.0) in this case.

Or, if you have an image stack taken from a single section at higher magnification, you’d want to enter the Z step of your image stack, and select the options used to acquire your image in focal/physical distance.

You are always welcome to open a support case if you have any questions.