How to measure nuclear cell ploidy level

Dear all,

I want to inquire about some tricky to measure the cell nuclear ploidy level. The attachment is the root tip stained with DAPI. I could get the nuclear surface mesh but it will still be many noise signal points. Is MGX able to delete mesh with definite size? And I want to measure nuclear area and density at the same time, could I do that? And how to use the signal function in the heat map list.

Thanks in advance.

1AB.tif (9.8 MB)

Do you have a wall marker as well? or just the DAPI?

It is just DAPI. Will it be only possible to get the signal result with the cell 3D mesh and nuclear mesh?

With a PM marker, you could segment the cells in 3D and count the signal from the DAPI inside the cells. If you really want to know the size of the nuclei, it is not really possible without a nuclear envelope marker. With a nuclear signal, turn up the gain, or lowering the threshold, will make the nuclei get bigger.

In MGX you can use Marching Cubes Surface to get a mesh around the nuclei, but you will find there will be lots of fused ones. As you turn up the threshold to eliminate that, you will start to miss a lot.

Probably the best way to do it is to extract the Local Maxima, and then use Mesh From Local Maxima. This will create little balls of a fixed size around the maxima, and you can then count the signal inside.

Thanks for your reply, I have tried, but it appeared like this…
snapshot.bmp (4.1 MB)

I get a voxel size of 3.082 in all dimensions with that stack, is that correct?

With those dimensions is used Gaussian Blur: 10, Local Maxima: 20, Mesh From Local Maxima: 20

You can see it does well in the elongation zone, but falls apart when it gets into the meristem towards the tip.

Bravo, but I still have no idea to set Local Maxima which parameter to 20?

In the process Stack/Segmentation/Local Maxima, set the X, Y, and Z radius to 10. The default threshold of 10000 seemed to work OK for me.

Then if I run a heat map on the volume and total signal, I get something like this, although I am not sure if it makes any sense.

I also made it! But I used the Gaussian Blur to 1 :sweat_smile: