You need to agree to share your contact information to access this dataset
This repository is publicly accessible, but you have to accept the conditions to access its files and content.
This dataset is in validation phase. Access is granted to verified researchers and organizations. Please describe your intended use case.
Log in or Sign Up to review the conditions and access this dataset content.
Microscopy Datasets Index
I kept losing track of which microscopy datasets exist and what format they're in. So I made an index. 300+ open datasets, searchable by domain, task, microscopy type, and license.
What's in here
A single reference file (JSONL and Parquet) cataloging 309 publicly available microscopy datasets. Each entry includes:
- id — short slug
- name — human-readable dataset name
- source — who published it (Broad Institute, Kaggle, ISBI, etc.)
- url — direct link to the dataset page
- domain — cell_biology, histopathology, materials_science, geology, parasitology, environmental, quality_control, botany, entomology
- task — instance_segmentation, image_classification, cell_tracking, object_detection, semantic_segmentation, etc.
- microscopy_type — fluorescence, brightfield, electron, phase_contrast, confocal, polarized_light, etc.
- image_count — approximate number of images
- license — CC0, CC-BY-4.0, Apache-2.0, etc.
- year — publication year
- notes — one-liner description
Coverage by domain
| Domain | Count |
|---|---|
| Cell Biology | ~110 |
| Histopathology | ~60 |
| Materials Science | ~25 |
| Quality Control | ~25 |
| Parasitology | ~20 |
| Geology | ~20 |
| Environmental | ~20 |
| Botany | ~15 |
| Entomology | ~15 |
What's included
- The full BBBC collection (Broad Bioimage Benchmark Collection, BBBC001-BBBC048)
- Cell Tracking Challenge datasets (15 sequences)
- Kaggle microscopy competitions (DSB 2018, Sartorius, HuBMAP, etc.)
- ISBI challenge datasets
- Human Protein Atlas collections
- Allen Cell Explorer datasets
- Recursion RxRx1/RxRx2/RxRx3
- JUMP-Cell Painting consortium
- TCGA histopathology (lung, breast, kidney, colon, prostate)
- Grand Challenge competitions (Camelyon, MoNuSeg, PanNuke, TIGER, MIDOG, etc.)
- Materials science: steel defects, metallography, SEM/EBSD, composites, additive manufacturing
- Geology: thin sections, digital rocks, micro-CT, petrology
- Parasitology: malaria, helminth eggs, trypanosomes, schistosoma
- Environmental: plankton, diatoms, microplastics, pollen
- Industrial QC: MVTec AD, steel surface defects, wafer maps, PCB defects
- Electron microscopy: CREMI, SNEMI3D, FIB-SEM, EMPIAR cryo-EM
Quick start
import pandas as pd
df = pd.read_parquet("data/microscopy_index.parquet")
# All fluorescence segmentation datasets
fluoro_seg = df[(df.microscopy_type == "fluorescence") & (df.task.str.contains("segmentation"))]
# Datasets with permissive licenses
open_data = df[df.license.isin(["CC0", "CC-BY-4.0", "Apache-2.0", "public-domain"])]
# Materials science datasets with 500+ images
big_materials = df[(df.domain == "materials_science") & (df.image_count >= 500)]
This is a reference index, not the actual data
The files here are a catalog. The URLs point to where the actual datasets live. I did not scrape or redistribute any images. If a URL is dead, open an issue and I'll update it.
Format
data/microscopy_index.jsonl— one JSON object per linedata/microscopy_index.parquet— same data, columnar format
Contributing
Know a microscopy dataset that's missing? Open a PR or issue with the dataset name, URL, and domain. I'll add it.
- Downloads last month
- 9