cff-version: 1.2.0
abstract: "<p>This repository contains a sample electron microscopy dataset produced with "FAST-EM array tomography" [1] and accompanying software to produce a 3D reconstruction of this dataset. FAST-EM array tomography is a technique for acquiring and reconstructing volume (3D) multibeam electron microscopy datasets. The sample dataset is part of a larger volume (3D) electron microscopy dataset included in the publication Kievits et al. (2024). This sample dataset is used for (automatic) testing of the software presented in the publication and as a demonstration example of 3D reconstruction.</p><p><br></p><p><strong>Datasets</strong></p><p><em>MCF-7 cells</em></p><p>3 serial sections of cultured Michigan Cancer Foundation-7 (MCF-7) cells (partial dataset). The dataset contains 25 images per section in a 5 x 5 grid, covering an area of 120 x 120 microns in each section of the sample. The `megafield_field_meta_data.yaml` contains metadata from the acquisition and is used in the processing.</p><p><br></p><p><em>Full dataset visualization</em></p><ul><li>Partial dataset link: <a href="https://webknossos.tnw.tudelft.nl/links/BIduioDOrpiBh_ED" target="_blank">https://webknossos.tnw.tudelft.nl/links/BIduioDOrpiBh_ED</a></li><li>Full dataset link: <a href="https://webknossos.tnw.tudelft.nl/links/9TwKDPdjNa4JHIYt" target="_blank">https://webknossos.tnw.tudelft.nl/links/9TwKDPdjNa4JHIYt</a></li></ul><p><br></p><p><em>Organization</em></p><p><br></p><p>┌ 20231107_MCF7_UAC_test (project)</p><p>├──┬ S001 (section --&gt; z)</p><p>│&nbsp;├── 000_000_0.tiff</p><p>│&nbsp;├── 000_001_0.tiff</p><p>│ ├── 000_002_0.tiff</p><p>│ │&nbsp;&nbsp;...</p><p>│ ├── 004_004_0.tiff</p><p>│ ├── mega_field_meta_data.yaml</p><p>├─── S002</p><p>└─── S003</p><p><br></p><p><strong>Software </strong></p><p><code>scripted-render-pipeline</code> : <a href="https://zenodo.org/doi/10.5281/zenodo.12733385" target="_blank">https://zenodo.org/doi/10.5281/zenodo.12733385</a></p><p>Automated pipeline for processing FAST-EM array tomography datasets</p><ul><li>Automated post-correction of images</li><li>Import to <code>render-ws</code></li><li>Export to (self-managed) <a href="https://webknossos.org/" target="_blank">WebKnossos</a> instances</li></ul><p><br></p><p><code>interactive-render-workflow</code>: <a href="https://zenodo.org/doi/10.5281/zenodo.12733814" target="_blank">https://zenodo.org/doi/10.5281/zenodo.12733814</a></p><p>Interactive workflow for aligning FAST-EM array tomography datasets</p><ul><li>Interactive post-correction of images</li><li>Import to <code>render-ws</code></li><li>Interactive 2D stitching</li><li>Interactive 3D alignment</li><li>Export to local WebKnossos instances</li></ul><p><br></p><p><code>fastem-sofima</code> : <a href="https://zenodo.org/doi/10.5281/zenodo.12733904" target="_blank">https://zenodo.org/doi/10.5281/zenodo.12733904</a></p><p>Scalable Optical Flow-based Image Montaging and Alignment (SOFIMA [2]) of FAST-EM array tomography datasets</p><p><br></p><p><strong>References</strong></p><p>[1] Kievits, Arent J., Duinkerken, B. H. Peter, Lane, Ryan, de Heus, Cecilia, van Beijeren Bergen en Henegouwen, Daan, Höppener, Tibbe, Wolters, Anouk H. G., Liv, Nalan, Giepmans, Ben N. G. and Hoogenboom, Jacob P.. "FAST-EM array tomography: a workflow for multibeam volume electron microscopy" <em>Methods in Microscopy</em>, 2024. <a href="https://doi.org/10.1515/mim-2024-0005" target="_blank">https://doi.org/10.1515/mim-2024-0005</a></p><p>[2] <a href="https://github.com/google-research/sofima" target="_blank">https://github.com/google-research/sofima</a></p><p><br></p><p><strong>License </strong></p><p>Data is published under a CC0 license. The software repositories are published under separate GPL-3.0 licenses.</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: Lane
    given-names: Ryan
    orcid: "https://orcid.org/0000-0002-5887-2069"
  - family-names: de Heus
    given-names: Cecilia 
    orcid: "https://orcid.org/0000-0001-8618-8451"
  - family-names: van Beijeren Bergen en Henegouwen
    given-names: Daan 
  - family-names: Höppener
    given-names: Tibbe 
  - family-names: H. G. Wolters
    given-names: Anouk
  - family-names: Liv
    given-names: Nalan
    orcid: "https://orcid.org/0000-0003-2654-9117"
  - family-names: Giepmans
    given-names: Ben N.G.
    orcid: "https://orcid.org/0000-0001-5105-5915"
  - family-names: Hoogenboom
    given-names: Jacob P.
    orcid: "https://orcid.org/0000-0003-4539-8772"
title: "Sample dataset and software for FAST-EM array tomography "
keywords:
version: 2
identifiers:
  - type: doi
    value: 10.4121/bf3f2b23-2328-4d81-a0f4-05fdb33117d7.v2
license: CC0
date-released: 2024-07-15