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Contributing

Thanks for helping keep this list useful. New datasets, new releases of existing ones, corrections, and dead-link reports are all welcome as an issue or a pull request.

What belongs here

  • Datasets acquired with volume electron microscopy (SBEM, FIB-SEM, GCIB-SEM, ATUM-SEM, multibeam SEM, ssTEM/TEMCA/autoTEM, serial-section ET, …) that anyone can view or download: raw image volumes, segmentations, synapse maps, proofread connectomes, or ground truth.
  • Benchmarks and challenges built on vEM data, and the pre-training corpora used to train foundation models on it.
  • Papers that describe one of the datasets above (they go into REFERENCE.md), plus reviews and methods that are essential for understanding them.
  • Non-EM connectomics (X-ray nanotomography, expansion microscopy) only as clearly marked context, not as dataset rows.

A dataset whose data cannot be accessed (not even through a viewer) can be listed, but please say so in the Note column.

Where to put things

You want to add File Section
A raw or reconstructed vEM volume DATASET.md the table for its organism (or Benchmark Cubes, Cell Biology)
Labeled data for training/evaluating models README.md Accessible Ground Truth
A challenge or benchmark with a leaderboard README.md Benchmarks and Challenges
The paper behind a dataset REFERENCE.md the heading for its publication year
A data portal, viewer or analysis tool README.md Data Portals and Tools / Related Code
A review or perspective README.md Reviews
A lab or company that produces vEM data GROUP.md alphabetical within its category

Conventions

  • Units: volume size in µm (x × y × z, e.g. 250x250x250; use mm3 for whole brains), voxel size in nm (x × y × z, e.g. 4x4x40).
  • Numbers: comma thousands separators (139,255 neurons); say what the number counts (neurons, cells, synapses, skeletons, instances).
  • Microscopy: use the abbreviations defined in BACKGROUND.md (e.g. SBEM, FIB-SEM, mSEM, ssTEM (GridTape)).
  • Order: newest first within a table; references newest first within a year.
  • Links: link the data itself (portal, bucket, DOI of the data deposit) in Link, and the paper via REFERENCE.md in Reference, using relative links such as REFERENCE.md#2025 so they also work in forks.
  • Preprints: mark them as (preprint) and update the entry once the paper is published.
  • Leave a cell empty rather than guessing; cite the source of any number you add.

Checklist for a pull request

  • The data link opens (or the note says how to request access).
  • The paper is in REFERENCE.md with a DOI link.
  • Units and abbreviations follow the conventions above.
  • The HTML tables still render (preview the Markdown before submitting).