Hi there, I am working with the 3dRoiManager and initially everything was going fine, but now I am experiencing some issues with the 3D Quantif function. Before that, I will explain a bit my procedure.
I have zStacks in two different channels of two different proteins expressed by a cell. I don’t have a cell marker, so I define some cell-like ROIs using a composite of the Max and I add them to the regular ROI Manager. Projections of the two channels. Then, I run the 3d object counter for each channel and I get an object map for each channel. Once that is ready, I open the 3d Manager and select one of the objetc map, then the first roi in the ROI manager and then I press Load Image in the 3d manager. I repeat the operation with the second Object Map. Consequently, I load only the objetcs from the two maps corresponding to one cell. Then I use the “Measure 3D” function or the “colocalization” and everything is fine.
The thing is that when I try to use Quantif 3D, I get NaNs for some objects. Does anybody know why thats happening?