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 1. 4TU.ResearchData. software. https://doi.org/10.4121/bf3f2b23-2328-4d81-a0f4-05fdb33117d7.v1

Software

x choose version: version 2 - 2024-07-15 (latest)

• Other Engineering
• Biochemistry and Cell Biology
• Optical Physics
• Engineering
• Physical Sciences
• Biological Sciences

array tomography, FAST-EM, image processing, volume electron microscopy

CC0

RefWorks, BibTeX, Reference Manager, Endnote, DataCite, NLM, DC, CFF

by Arent J. Kievits , B. H. Peter Duinkerken , Ryan Lane , Cecilia de Heus , Daan van Beijeren Bergen en Henegouwen , Tibbe Höppener , Anouk H. G. Wolters , Nalan Liv , Ben N.G. Giepmans , Jacob P. Hoogenboom

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)] (DOI will be added). 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://github.com/hoogenboom-group/scripted-render-pipeline

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://github.com/hoogenboom-group/interactive-render-workflow

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://github.com/hoogenboom-group/fastem-sofima

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

References

[1] ref to paper (accepted in MiM, will be added once online)

[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.

• 2024-07-02 first online, published, posted

4TU.ResearchData

TIFF

• 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

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