Datasets › Electron Microscopy Dataset
Electron Microscopy Dataset
The dataset available for download on this webpage represents a 5x5x5µm section taken from the CA1 hippocampus region of the brain, corresponding to a 1065x2048x1536 volume. The resolution of each voxel is approximately 5x5x5nm. The data is provided as multipage TIF files that can be loaded in Fiji. We annotated mitochondria in two sub-volumes. Each sub-volume consists of the first 165 slices of the 1065x2048x1536 image stack. The volume used for training our algorithm in the publications mentionned at the bottom of this page is the top part while the bottom part was used for testing.
Although our line of research was primarily motivated by the need to accurately segment mitochondria and synapses, other structures are of interest for neuroscientists such as vesicles or cell boundaries. This dataset was acquired by Graham Knott and Marco Cantoni at EPFL. It is made publicly available in the hope of encouraging similar sharing of useful data amongst researchers and also accelerating neuroscientific research.
Benchmarks archive 2025-07-28
All 1 leaderboard whose dataset resolves to this page shown (sort by any header). "First row" is the archive's own first row at snapshot, in the archive's row order; nothing here re-ranks and metric direction is not asserted.
| First row (archive order) | Paper | Code | ||||
|---|---|---|---|---|---|---|
| Medical Image Segmentation | Electron Microscopy Dataset | ReN-UNet AHD95 5.3703 | Rethinking the Nested U-Net Approach: Enhancing... | saadwazir/ReN-UNet | 1 | Compare |
Papers archive 2025-07-28
1 shown of 1 paper with a leaderboard row on this dataset's benchmarks, newest first. The archive's own "papers using this dataset" list was never published, so this is the benchmark-backed subset; the archive's count for this dataset is 2. The Syntology column is from Syntology's graph (read 2026-09-24), stated per sample; it is not part of any archive number.
| Date | Samples run Syntology | |||
|---|---|---|---|---|
| Rethinking the Nested U-Net Approach: Enhancing Biomarker Segmentation with Attention Mechanisms and Multiscale Feature Fusion | 1 | 1 | 8 Apr 2025 | not harvested |
Dataset loaders archive 2025-07-28
No loader listed in the archive.
Tasks archive 2025-07-28
License archive 2025-07-28
No licence recorded in the archive. Absence here is not a statement about the dataset's terms.
Modalities archive 2025-07-28
Languages archive 2025-07-28
No language tagged.
Variants archive 2025-07-28
- Electron Microscopy Dataset
1 variant name, as the archive lists them.
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