| --- |
| license: apache-2.0 |
| task_categories: |
| - image-classification |
| - image-segmentation |
| - object-detection |
| tags: |
| - microscopy |
| - bioimage |
| - histopathology |
| - cell-biology |
| - materials-science |
| - dataset-index |
| - meta-dataset |
| size_categories: |
| - n<1K |
| pretty_name: Microscopy Datasets Index |
| extra_gated_prompt: >- |
| This dataset is in validation phase. |
| Access is granted to verified researchers and organizations. |
| Please describe your intended use case. |
| extra_gated_fields: |
| Full name: text |
| Organization: text |
| Intended use: text |
| I agree to use this data for research purposes only: |
| type: checkbox |
| --- |
| |
| # 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 |
|
|
| ```python |
| 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 line |
| - `data/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. |
|
|
