datasets
Training and evaluation data, with the modality, task and licence stated up front. Listed live from the Hugging Face Hub.
Lurcher_10x
Lurcher 10x Microscopy Dataset
Dataset overview
This dataset consists of 2-D microscopy images of histologically stained 3-D structures in tissue sections through the cerebellum of 21 mouse brains. Animals are grouped into wild-type controls (n = 10) and Lurcher mutant mice (n = 11). The classification task is to distinguish Lurcher mutant mice from wild-type controls.
All images were captured at low magnification (10x) and stained with Cresyl violet, a general… See the full description on the dataset page: https://huggingface.co/datasets/USF-CS-Microscopy-Image-Analysis/Lurcher_10x.phytoplankton-microscopy
Bloombio Phytoplankton Microscopy Dataset
The Bloombio Phytoplankton Microscopy Dataset is a curated, citable marine science dataset consisting of 43 phytoplankton species across 10,433 high-resolution light microscopy images with bounding box annotations.
Developed as part of the Bloombio Marine Intelligence Platform — a platform that equips scientists with an autonomous AI agent, compressing sampling setup, multi-modal species identification, and environmental risk assessment… See the full description on the dataset page: https://huggingface.co/datasets/bloombio/phytoplankton-microscopy.biomedica_microscopy_imagining_subset_parquet
Dataset Card for "biomedica_microscopy_imagining_subset_parquet"
More Information needed
malaria-microscopy-vqa
Malaria Microscopy Visual Question Answering (VQA) Dataset
Dataset Description
This dataset contains multi-choice visual question answering pairs for malaria microscopy images, focusing on parasite detection, classification, species identification, and severity assessment.
Dataset Summary
The Malaria Microscopy VQA Dataset is designed for training and evaluating AI systems on medical microscopy image analysis tasks. It contains 67 questions across 59 unique… See the full description on the dataset page: https://huggingface.co/datasets/EricPeter/malaria-microscopy-vqa.Electron_microscopy_datasetThe dataset:
Is a patch from the existing dataset available at https://www.epfl.ch/labs/cvlab/data/data-em/.
Contains patches of size (256, 256).
Removes any patches with empty masks to ensure quality.
Has the same license applied as the original dataset.
Please refer to the license for information on allowed usage.
If you have any questions or concerns about the dataset, please do not hesitate to contact me.
biomedica_microscopy_subset_webdatasetSingle-cell_Microscopy_Images_for_Cancer_ClassificationThis datatset is a mirror to the dataset "Single-cell Microscopy Images for Cancer Classification" DOI: "xxxxxxx" in Mendeley Data, we will maintain both to upload new dataset in time and keep these two versions the same.
This is a dataset for single cell fluorescence microscopy images. The dataset includes cancer cells and normal cells. The images contain three channels: red (actin filament), green (vimentin filament), and blue (nucleus). We have 591 normal cells and 542 cancer cells. More… See the full description on the dataset page: https://huggingface.co/datasets/Jiabang/Single-cell_Microscopy_Images_for_Cancer_Classification.brightfield-microscopy-scc
Brightfield Microscopy SCC Dataset
Dataset Description
The Brightfield Microscopy SCC Dataset contains brightfield microscopy images that have been sliced from 4K resolution images. The cells in the images are labeled with bounding boxes. This dataset is used for training unconditional diffusion models and cell detection models.
Dataset Structure
The dataset is organized into the following splits:
train: 27,161 examples
validation: 3,302 examples
test: 1,580… See the full description on the dataset page: https://huggingface.co/datasets/mario-dg/brightfield-microscopy-scc.NEU-Feces-Microscopy-Datasetafrica-synth-malaria-malaria-rdt-microscopy-all
Malaria RDT & Microscopy | Africa (World Health Organization)
Size category: 10K<n<100K - Formats: csv - Sector: health - Engineered by Electric Sheep Africa
TL;DR
This dataset is part of the Electric Sheep Africa catalog on Hugging Face. It is indexed for African data discovery with standardized metadata, loading guidance, provenance notes, and analyst-oriented context.
What This Dataset Covers
Health datasets help researchers examine disease… See the full description on the dataset page: https://huggingface.co/datasets/electricsheepafrica/africa-synth-malaria-malaria-rdt-microscopy-all.microscopy_imagesmicrovqa-microscopy-reasoning
MicroVQA - Microscopy Visual Question Answering
MicroVQA 显微镜生物学视觉问答数据集
Description
MicroVQA (Visual Question Answering) examines model reasoning capabilities in microscopy-based biological research. Models must simultaneously understand image content and natural language questions, generating accurate text answers.
Key Features:
Expert-Driven: Question chains designed by biologists with 5+ years of experience, ensuring research authenticity
Progressive Difficulty: Same… See the full description on the dataset page: https://huggingface.co/datasets/obaydata/microvqa-microscopy-reasoning.brightfield-microscopy-scc-filtered
Brightfield Microscopy SCC Dataset
Filtered to only contain images with no well edge visible
Dataset Description
The Brightfield Microscopy SCC Dataset contains brightfield microscopy images that have been sliced from 4K resolution images. The cells in the images are labeled with bounding boxes. This dataset is used for training unconditional diffusion models and cell detection models.
Dataset Structure
The dataset is organized into the following splits:… See the full description on the dataset page: https://huggingface.co/datasets/mario-dg/brightfield-microscopy-scc-filtered.clip_microscopy_image_text_embeddingsrocov2-modality-microscopy
ROCOv2 Microscopy Dataset
This dataset contains Microscopy imaging data from the ROCOv2 radiology dataset.
Dataset Structure
caption: Medical description text
modality: Imaging modality (Microscopy)
modality_id: Numerical modality ID
caption_length: Number of words in caption
length_category: Short/medium/long categorization
original_index: Index from original dataset
Splits
train: 162 samples
val: 20 samples
test: 21 samples
Usage
from… See the full description on the dataset page: https://huggingface.co/datasets/WafaaFraih/rocov2-modality-microscopy.microscopygpt_jarvisdft_2dmicroscopygpt_jarvisdft_2dafrica-who-number-of-malaria-suspects-examined-by-microscopy
Africa — WHO GHO: Number of malaria suspects examined by microscopy | Africa (World Health Organization)
Size category: n<1K - Formats: parquet - Sector: health - Engineered by Electric Sheep Africa
TL;DR
This dataset is part of the Electric Sheep Africa catalog on Hugging Face. It is indexed for African data discovery with standardized metadata, loading guidance, provenance notes, and analyst-oriented context.
What This Dataset Covers
Health… See the full description on the dataset page: https://huggingface.co/datasets/electricsheepafrica/africa-who-number-of-malaria-suspects-examined-by-microscopy.africa-who-number-of-malaria-positive-cases-by-microscopy
Africa — WHO GHO: Number of malaria positive cases by microscopy | Africa (World Health Organization)
Size category: n<1K - Formats: parquet - Sector: health - Engineered by Electric Sheep Africa
TL;DR
This dataset is part of the Electric Sheep Africa catalog on Hugging Face. It is indexed for African data discovery with standardized metadata, loading guidance, provenance notes, and analyst-oriented context.
What This Dataset Covers
Health… See the full description on the dataset page: https://huggingface.co/datasets/electricsheepafrica/africa-who-number-of-malaria-positive-cases-by-microscopy.asia-who-number-of-malaria-suspects-examined-by-microscopy
Africa — WHO GHO: Number of malaria suspects examined by microscopy
Indicator code: MALARIA_MICR_TEST
HuggingFace slug: electricsheepafrica/asia-who-number-of-malaria-suspects-examined-by-microscopy
Source: WHO Global Health Observatory
License: CC BY 4.0 — WHO Open Data
Dataset Description
This dataset contains country-level observations for the WHO GHO indicator "Number of malaria suspects examined by microscopy" (MALARIA_MICR_TEST) across Asian nations, spanning… See the full description on the dataset page: https://huggingface.co/datasets/electricsheepasia/asia-who-number-of-malaria-suspects-examined-by-microscopy.clip_microscopy_img_embeddingsasia-who-number-of-malaria-positive-cases-by-microscopy
Africa — WHO GHO: Number of malaria positive cases by microscopy
Indicator code: MALARIA_MICR_POS
HuggingFace slug: electricsheepafrica/asia-who-number-of-malaria-positive-cases-by-microscopy
Source: WHO Global Health Observatory
License: CC BY 4.0 — WHO Open Data
Dataset Description
This dataset contains country-level observations for the WHO GHO indicator "Number of malaria positive cases by microscopy" (MALARIA_MICR_POS) across Asian nations, spanning 2015–2024.… See the full description on the dataset page: https://huggingface.co/datasets/electricsheepasia/asia-who-number-of-malaria-positive-cases-by-microscopy.Expansion-microscopymineral-thin-section-microscopymicroscopy-parasitesmicroscopy-demomicroscopy-100k-patchedmicroscopy-focus-testset
Insect Microscopy Multi-Focus Test Set
This repository contains an insect microscopy multi-focus test set for evaluating dual-focus and multi-focus image fusion methods. The dataset includes microscopy focus-stack TIFF sequences with fused reference images where available, plus additional JPEG microscopy image series. File and directory names are organized with neutral sample identifiers for reproducible evaluation.
The dataset is intended for academic research on microscopy… See the full description on the dataset page: https://huggingface.co/datasets/Data-set/microscopy-focus-testset.Microscopy-Dataset
1. CellProfiler-Training (12 training modules)
Educational content with problem statements and guided solutions:
ExampleColocalization: Colocalization training
ExampleCometAssay: Comet assay training
ExampleImagingFlowCytometryObjectsInGrid: Flow cytometry training
ExamplePercentPositive: Percentage analysis training
ExampleTrackObjects: Object tracking training
ExampleWoundHealing: Wound healing training
Tutorial3DFISH: 3D FISH analysis
Tutorial3DMonolayer: 3D monolayer… See the full description on the dataset page: https://huggingface.co/datasets/orion-agent/Microscopy-Dataset.microscopy-datasets-index
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… See the full description on the dataset page: https://huggingface.co/datasets/Laborator/microscopy-datasets-index.