Depth Correction of TOF-SIMS Depth Profiling Images Using the Total Ion Count Images

Depth profiling time of flight secondary ion mass spectrometry (TOF-SIMS) enables imaging the distributions of unlabeled metabolites within cells. When depth profiling TOF-SIMS is performed on intact cells, the 3D renderings produced by stacking and rending the individual depth profiling images are distorted along the z-axis, which complicates image interpretation. Here we describe an approach for correcting the z-axis distortion in 3D TOF-SIMS depth profiling images of cells. This approach uses the total ion images collected during TOF-SIMS depth profiling to create a 3D morphology model of the cell’s surface at the time when each depth profiling image was acquired. These morphology models are used to correct the z-position and height of each voxel in the component-specific 3D TOF-SIMS images. We have applied this approach to 3D TOF-SIMS depth profiling images that show endoplasmic reticulum-plasma membrane (ER-PM) junctions in cells that are a simplified model of ER-PM junctions in neuronal cells. The depth corrected 3D image more accurately depicted the structure of the ER-PM junctions than the uncorrected image. Projection of the depth corrected 3D image on the model of the cell’s morphology facilitated visualization of the ER-PM junctions relative to the peaks, ridges and valleys on the surface of the cell. Thus, accurate component-specific 3D images may now be produced for depth profiling TOF-SIMS datasets. This approach may facilitate efforts to identify the lipids and other metabolites that reside in ER-PM junctions in neuronal cells and elucidate their roles in neuronal function.