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)] (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.<br><strong>Datasets</strong><em>MCF-7 cells</em>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.<br><em>Full dataset visualization</em>[Partial dataset link](https://webknossos.tnw.tudelft.nl/links/BIduioDOrpiBh_ED) [Full dataset link](https://webknossos.tnw.tudelft.nl/links/9TwKDPdjNa4JHIYt)<br><em>Organization</em><br>┌ 20231107_MCF7_UAC_test (project)├──┬ S001 (section --&gt; z)│ ├── 000_000_0.tiff│ ├── 000_001_0.tiff│ ├── 000_002_0.tiff│ │  ...│ ├── 004_004_0.tiff│ ├── mega_field_meta_data.yaml├─── S002└─── S003<br><strong>Software </strong><code>scripted-render-pipeline</code> : https://github.com/hoogenboom-group/scripted-render-pipelineAutomated pipeline for processing FAST-EM array tomography datasetsAutomated post-correction of imagesImport to <code>render-ws</code>Export to (self-managed) WebKnossos instances<br><code>interactive-render-workflow</code>: https://github.com/hoogenboom-group/interactive-render-workflowInteractive workflow for aligning FAST-EM array tomography datasetsInteractive post-correction of imagesImport to <code>render-ws</code>Interactive 2D stitchingInteractive 3D alignmentExport to local WebKnossos instances<br><code>fastem-sofima</code> : https://github.com/hoogenboom-group/fastem-sofimaScalable Optical Flow-based Image Montaging and Alignment (SOFIMA [2]) of FAST-EM array tomography datasets<br><strong>References</strong>[1] ref to paper (accepted in MiM, will be added once online)[2] https://github.com/google-research/sofima<br><strong>License </strong>Data is published under a CC0 license. The software repositories are published under separate GPL-3.0 licenses.<br><br>