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.
FAST-EM array tomography: a workflow for multibeam volume electron microscopy