Datasets:

Laborator
/

microscopy-datasets-index

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

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.