Microscopy data, code and analysis underlying the publication "Optical STEM detection for scanning electron microscopy"

doi: 10.4121/9c98aee1-608e-4c71-8b89-dcb1e8eb3e5e.v2
The doi above is for this specific version of this dataset, which is currently the latest. Newer versions may be published in the future. For a link that will always point to the latest version, please use
doi: 10.4121/9c98aee1-608e-4c71-8b89-dcb1e8eb3e5e
Datacite citation style:
Kievits, Arent J.; Duinkerken, B. H. Peter; Fermie, Job ; Lane, Ryan; Giepmans, Ben N.G. et. al. (2023): Microscopy data, code and analysis underlying the publication "Optical STEM detection for scanning electron microscopy". Version 2. 4TU.ResearchData. software. https://doi.org/10.4121/9c98aee1-608e-4c71-8b89-dcb1e8eb3e5e.v2
Other citation styles (APA, Harvard, MLA, Vancouver, Chicago, IEEE) available at Datacite
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version 2 - 2023-10-31 (latest)
version 1 - 2023-10-16

Raw microscopy data underlying the publication, structured per experiment (figure). The imaging setting that is varied in the experiments (exposure/dwell time, beam current, landing energy) is indicated by the folder or image name. The images may have a data bar indicating the relevant acquisition settings.

  • For more information on the sample preparation and image acquisition, see the Methodology section in the publication.
  • The code and data analysis notebooks are included in the accompanying Github repository: https://github.com/hoogenboom-group/Kievits-OSTEM-2023

Data set structure:

  • 1_Optimization-OSTEM: contains the images for the landing energy optimization (Figure 2 in the article). Images have a pixel size of 1 nm and where acquired with increments of 500 eV (electron volts). Dwell times are indicated in the folder names. The 'Qualitative' folder contains a subset of these data for ease of plotting Figure 2A.
  • 2_Qualitative-comparison: contains qualitative images of rat pancreas and zebrafish larva (Figure 3). Both raw images (with metadata in TIFF header) and cropped images are included (used for publication). Images have a pixel size of 4 nm.
  • 3_SNR-comparison-detectors: contains images used for the quantitative comparison of detectors (Figure 4). Contains a folder per detection technique with all the images. The 'Qualitative' folder contains a subset of these data for ease of plotting Figure 4A.
  • 4_Image-resolution-detectors: contains raw images and extracted edge widths from FEI Image (Figure 5). The acquisition settings are indicated in the folder names, with one folder per detection technique.
  • 5_Current-SNR-relation: contains the images with increasing beam current / fixed dwell time and increasing dwell time / fixed current (Figure 6). The 'Qualitative' folder contains a subset of the data for ease of plotting Figure 6A and 6B.
  • 6_Supplementary: contains the supplementary data, used for the background texture analysis. The results in Figure S4 and Table S1 are based on these images.

General acquisition parameters

Pixel size = 1 nm (unless stated otherwise)

Beam current = 0.4nA (unless stated otherwise)

BSD, SE Landing energy = 1.5keV (typically)

OSTEM landing energy = 4keV (typically)

ADF-STEM landing energy = 25keV

  • 2023-10-16 first online
  • 2023-10-31 published, posted
associated peer-reviewed publication
Optical STEM detection for scanning electron microscopy
  • ZonMw (grant code 91111.006) [more info...] ZonMw
  • NWO National Roadmap for Large-Scale Research Infrastructure of the Dutch Research Council (NWO 184.034.014)
  • NWO-LIFT (grant code ENPPS.LIFT.019.030) [more info...] NWO
  • EFRO Kansen voor West [more info...] EU-REACT
TU Delft, Faculty of Applied Sciences, Department of Imaging Physics


To access the source code, use the following command:

git clone https://data.4tu.nl/v3/datasets/e9adfc91-018d-4156-a7c1-189643e4c3b7.git
files (2)