Electron_Microscopy-Data_Engineering

This repository documents a series of data engineering tasks focused on several large-scale 3D Electron Microscopy (EM) datasets from different sources.

Summary

The main objectives were:

• Automated Data Downloading: Developed code and workflows to efficiently download large volumetric datasets from public repositories.
• Metadata Extraction: Extracted and consolidated relevant metadata from each dataset into a Markdown/CSV file
• Dataset Organization: Structured the repo in such a way that each dataset has a dedicated folder, with methods and detailed notes for data access and metadata extraction described in the respective folders.

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Datasets Overview

For detailed documentation, methods, and metadata fields for each dataset, see the README file in the respective folder.

• OpenOrganelle (jrc_mus-nacc-2):
  See Open_Organelle/README.md.

• Neuroglancer Hemibrain:
  See Neuroglancer/README.md

• IDR 9846137:
  See IDR/README.md.

• Zebrafish - EMPIAR 11759:
  See EMPIAR/README.md for dataset information.

• EPFL Electron Microscopy:
  See EPFL/README.md.

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