Analysis of depth-sectioning STEM for thick samples and 3D imaging
Related Experiment Video
Updated: Jan 20, 2026

A Sectioning, Coring, and Image Processing Guide for High-Throughput Cortical Bone Sample Procurement and Analysis for Synchrotron Micro-CT
Published on: June 12, 2020
1Thermo Fisher Scientific, Achtseweg, Noord 5, 5651GG Eindhoven, NOORD-BRABANT, the Netherlands.
Abstract:
We derive a model that describes 3D volume imaging in depth-sectioning STEM that is valid for all STEM techniques under three well-defined conditions: linearity, undisturbed probe and elastic scattering. The resulting undisturbed probe model generalizes the widely used idea that the undisturbed probe intensity in three dimensions can be used as the point spread function for depth-sectioning ADF-STEM to all STEM techniques including (A)BF- and iDPC-STEM. The model provides closed expressions for depth-sectioning STEM, which follow directly from the 2D expressions for thin samples, and thereby enables analysis of the 3D resolution. Using the model we explore the consequences of the resulting 3D contrast transfer function (CTF) for the z-resolution at different length scales and illustrate this with experiments. We investigate the validity and limitations of the model using multi-slice simulations showing that it is valid and quantitatively accurate for relatively thick amorphous samples but not for crystalline samples in zone-axis due to channeling. We compare depth-sectioning in iDPC- and ADF-STEM and show that iDPC-STEM can extract information from deeper into the sample, all the way till the bottom of the sample, thereby effectively allowing a thickness measurement. Also the difference in optimal focus conditions between iDPC- and ADF-STEM is explained. Finally, we propose practical criteria for deciding whether a sample is thin or thick.
More Related Videos
11:24High-throughput Imaging and Analysis Workflow for Evaluating Skin Cell Phenotypes and Proliferation States in Tissue Samples
Published on: October 31, 2025
10:55Procedure for the Development of Multi-depth Circular Cross-sectional Endothelialized Microchannels-on-a-chip
Published on: October 21, 2013
Related Concept Videos
07:10A Sectioning, Coring, and Image Processing Guide for High-Throughput Cortical Bone Sample Procurement and Analysis for Synchrotron Micro-CT
11:24High-throughput Imaging and Analysis Workflow for Evaluating Skin Cell Phenotypes and Proliferation States in Tissue Samples
10:55Procedure for the Development of Multi-depth Circular Cross-sectional Endothelialized Microchannels-on-a-chip
15:53Utilizing 3D Printing Technology to Merge MRI with Histology: A Protocol for Brain Sectioning
07:103D Depth Profile Reconstruction of Segregated Impurities Using Secondary Ion Mass Spectrometry
06:42Cerebrovascular Casting of the Adult Mouse for 3D Imaging and Morphological Analysis