cff-version: 1.2.0
abstract: "<p>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.</p><ul><li>For more information on the sample preparation and image acquisition, see the Methodology section in the publication.</li><li>The code and data analysis notebooks are included in the accompanying Github repository: https://github.com/hoogenboom-group/Kievits-OSTEM-2023</li></ul><p><br></p><p>Data set structure:</p><ul><li><strong>1_Optimization-OSTEM</strong>: 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.</li><li><strong>2_Qualitative-comparison</strong>: 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.</li><li><strong>3_SNR-comparison-detectors: </strong>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.</li><li><strong>4_Image-resolution-detectors</strong>: 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.</li><li><strong>5_Current-SNR-relation: </strong>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.</li><li><strong>6_Supplementary</strong>: contains the supplementary data, used for the background texture analysis. The results in Figure S4 and Table S1 are based on these images.</li></ul><p><br></p><p><strong>General acquisition parameters</strong></p><p>Pixel size = 1 nm (unless stated otherwise)</p><p>Beam current = 0.4nA (unless stated otherwise)</p><p>BSD, SE Landing energy = 1.5keV (typically)</p><p>OSTEM landing energy = 4keV (typically)</p><p>ADF-STEM landing energy = 25keV</p><p><br></p><p><br></p><p><br></p><p><br></p><p><br></p>"
authors:
  - family-names: Kievits
    given-names: Arent J.
    orcid: "https://orcid.org/0000-0003-4457-9627"
  - family-names: Duinkerken
    given-names: B. H. Peter
    orcid: "https://orcid.org/0000-0003-0699-0001"
  - family-names: Fermie
    given-names: Job 
    orcid: "https://orcid.org/0000-0002-7340-0377"
  - family-names: Lane
    given-names: Ryan
    orcid: "https://orcid.org/0000-0002-5887-2069"
  - family-names: Giepmans
    given-names: Ben N.G.
    orcid: "https://orcid.org/0000-0001-5105-5915"
  - family-names: Hoogenboom
    given-names: Jacob
    orcid: "https://orcid.org/0000-0003-4539-8772"
title: "Microscopy data, code and analysis underlying the publication &#34;Optical STEM detection for scanning electron microscopy&#34;"
keywords:
version: 2
identifiers:
  - type: doi
    value: 10.4121/9c98aee1-608e-4c71-8b89-dcb1e8eb3e5e.v2
license: CC BY 4.0
date-released: 2023-10-31