Getting NaNs after 3d Quantif in 3DRoiManager

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?



Hi @leboero,

To use Quantif 3D you need to select on which image you want to measure signal statistics. In case the objects selected for quantification do not fit into the image, you may get some NaN values. Check you selected the right image for quantification.

Hope this helps