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_ED
Full 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 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.