Sample dataset and software for FAST-EM array tomography

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 [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.