Sample dataset and software for FAST-EM array tomography

doi:10.4121/bf3f2b23-2328-4d81-a0f4-05fdb33117d7.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/bf3f2b23-2328-4d81-a0f4-05fdb33117d7
Datacite citation style:
Kievits, Arent J.; Duinkerken, B. H. Peter; Lane, Ryan; de Heus, Cecilia ; van Beijeren Bergen en Henegouwen, Daan et. al. (2024): Sample dataset and software for FAST-EM array tomography . Version 2. 4TU.ResearchData. software. https://doi.org/10.4121/bf3f2b23-2328-4d81-a0f4-05fdb33117d7.v2
Other citation styles (APA, Harvard, MLA, Vancouver, Chicago, IEEE) available at Datacite
Software
choose version:
version 2 - 2024-07-15 (latest)
version 1 - 2024-07-02

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


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 images
  • Import to render-ws
  • Export 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 images
  • Import to render-ws
  • Interactive 2D stitching
  • Interactive 3D alignment
  • Export to local WebKnossos instances


fastem-sofima : https://zenodo.org/doi/10.5281/zenodo.12733904

Scalable Optical Flow-based Image Montaging and Alignment (SOFIMA [2]) of FAST-EM array tomography datasets


References

[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" Methods in Microscopy, 2024. https://doi.org/10.1515/mim-2024-0005

[2] https://github.com/google-research/sofima


License

Data is published under a CC0 license. The software repositories are published under separate GPL-3.0 licenses.



history
  • 2024-07-02 first online
  • 2024-07-15 published, posted
publisher
4TU.ResearchData
format
TIFF
funding
  • ZonMw grant 91111.006 (grant code 91111.006) ZonMw
  • Netherlands Electron Microscopy Infrastructure (NEMI) (grant code 184.034.014) NWO National Roadmap for Large-Scale Research Infrastructure
  • NWO-ENPPS.LIFT.019.030 (grant code LIFT.019.030) NWO
  • EFRO Kansen voor West [more info...] EU-REACT
  • Nano Metrology Systems project National Growth Fund, NXTGEN HIGHTECH
organizations
TU Delft, Faculty of Applied Sciences, Department of Imaging Physics
University Medical Center Groningen, Department of Biological Sciences
University Medical Center Utrecht, Center for Molecular Medicine

DATA

files (2)