SoftwareApplication
name: Sample dataset and software for FAST-EM array tomography
description: Sample dataset and software for FAST-EM array tomography
description: 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. Datasets MCF-7 cells 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. Full dataset visualization Partial dataset link: https://webknossos.tnw.tudelft.nl/links/BIduioDOrpiBh_EDFull dataset link: https://webknossos.tnw.tudelft.nl/links/9TwKDPdjNa4JHIYt Organization ┌ 20231107_MCF7_UAC_test (project) ├──┬ S001 (section --> z) │ ├── 000_000_0.tiff │ ├── 000_001_0.tiff │ ├── 000_002_0.tiff │ │ ... │ ├── 004_004_0.tiff │ ├── mega_field_meta_data.yaml ├─── S002 └─── S003 Software scripted-render-pipeline : https://zenodo.org/doi/10.5281/zenodo.12733385 Automated pipeline for processing FAST-EM array tomography datasets Automated post-correction of imagesImport to render-wsExport to (self-managed) WebKnossos instances interactive-render-workflow: https://zenodo.org/doi/10.5281/zenodo.12733814 Interactive workflow for aligning FAST-EM array tomography datasets Interactive post-correction of imagesImport to render-wsInteractive 2D stitchingInteractive 3D alignmentExport to local WebKnossos instances fastem-sofima : https://zenodo.org/doi/10.5281/zenodo.12733904 Scalable Optical Flow-based Image Montaging and Alignment (SOFIMA […
author: https://orcid.org/0000-0003-4457-9627
author: https://orcid.org/0000-0003-0699-0001
author: https://orcid.org/0000-0002-5887-2069
author: https://orcid.org/0000-0001-8618-8451
author: Person
  given name: Daan
  family name: van Beijeren Bergen en Henegouwen
  name: Daan van Beijeren Bergen en Henegouwen
author: Person
  given name: Tibbe
  family name: Höppener
  name: Tibbe Höppener
author: Person
  given name: Anouk
  family name: H. G. Wolters
  name: Anouk H. G. Wolters
author: https://orcid.org/0000-0003-2654-9117
author: https://orcid.org/0000-0001-5105-5915
author: https://orcid.org/0000-0003-4539-8772
keywords: Volume Electron Microscopy
keywords: Image processing
keywords: array tomography
keywords: FAST-EM
license:
  creative work: creativeWork
    name: CC0-1.0
reference publication: mim-2024-0005

https://orcid.org/0000-0003-4457-9627
type: Person
given name: Arent J.
family name: Kievits
name: Arent J. Kievits

https://orcid.org/0000-0003-0699-0001
type: Person
given name: B. H. Peter
family name: Duinkerken
name: B. H. Peter Duinkerken

https://orcid.org/0000-0002-5887-2069
type: Person
given name: Ryan
family name: Lane
name: Ryan Lane

https://orcid.org/0000-0001-8618-8451
type: Person
given name: Cecilia
family name: de Heus
name: Cecilia de Heus

https://orcid.org/0000-0003-2654-9117
type: Person
given name: Nalan
family name: Liv
name: Nalan Liv

https://orcid.org/0000-0001-5105-5915
type: Person
given name: Ben N.G.
family name: Giepmans
name: Ben N.G. Giepmans

https://orcid.org/0000-0003-4539-8772
type: Person
given name: Jacob P.
family name: Hoogenboom
name: Jacob P. Hoogenboom

mim-2024-0005
type: ScholarlyArticle
name: FAST-EM array tomography: a workflow for multibeam volume electron microscopy
pagination: 49-64
url: https://doi.org/10.1515%2Fmim-2024-0005