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https://github.com/sfikas/medical-imaging-datasets

A list of Medical imaging datasets.
https://github.com/sfikas/medical-imaging-datasets

image-dataset medical-imaging

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A list of Medical imaging datasets.

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# medical-imaging-datasets



* A list of Medical imaging datasets. Source : https://sites.google.com/site/aacruzr/image-datasets

* An additional, possibly overlapping list can be found at : https://github.com/beamandrew/medical-data



### Multimodal databases



* Center for Invivo Microscopy (CIVM), Embrionic and Neonatal Mouse (H&E, MR) http://www.civm.duhs.duke.edu/devatlas/ 

user guide: http://www.civm.duhs.duke.edu/devatlas/UserGuide.pdf

* LONI image data archive https://ida.loni.usc.edu/services/Menu/IdaData.jsp?project=

* Radiology (Ultrasound, Mammographs, X-Ray, CT, MRI, fMRI, etc.)

* Collaborative Informatics and Neuroimaging Suite (COINS) https://portal.mrn.org/micis/index.php?subsite=dx

* The Cancer Imaging Archive (TCIA) http://www.cancerimagingarchive.net/ (Collections)

* Alzheimer’s Disease Neuroimaging Initiative (ADNI) http://adni.loni.ucla.edu/

* The Open Access Series of Imaging Studies (OASIS) http://www.oasis-brains.org/

* Breast Cancer Digital Repository https://bcdr.eu/

* DDSM: Digital Database for Screening Mammography http://marathon.csee.usf.edu/Mammography/Database.html

* The Mammographic Image Analysis Society (MIAS) mini-database http://peipa.essex.ac.uk/info/mias.html

* Mammography Image Databases 100 or more images of mammograms with ground truth. Additional images available by request, and links to several other mammography databases are provided http://marathon.csee.usf.edu/Mammography/Database.html

* NLM HyperDoc Visible Human Project color, CAT and MRI image samples - over 30 images http://www.nlm.nih.gov/research/visible/visible_human.html

* CT Scans for Colon Cancer https://wiki.cancerimagingarchive.net/display/Public/CT+COLONOGRAPHY#e88604ec5c654f60a897fa77906f88a6

* [[BreastScreening](http://breastscreening.github.io/)] UTA4: Breast Cancer Medical Imaging DICOM Files Dataset & Resources (MG, US and MRI) https://github.com/MIMBCD-UI/dataset-uta4-dicom

* [[MIMBCD-UI](http://mimbcd-ui.github.io/)] UTA7: Breast Cancer Medical Imaging DICOM Files Dataset & Resources (MG, US and MRI) https://github.com/MIMBCD-UI/dataset-uta7-dicom

* [[Facebook AI + NYU FastMRI](https://fastmri.org/dataset/)] includes two types of MRI scans: knee MRIs and the brain (neuro) MRIs, containing training, validation, and masked test sets. Also includes PyTorch data loaders in open-sourced [GitHub Repository](https://github.com/facebookresearch/fastMRI/)

* BCNB: Early Breast Cancer Core-Needle Biopsy WSI Dataset, https://bupt-ai-cz.github.io/BCNB/, https://github.com/bupt-ai-cz/BALNMP#bcnb-dataset

* National Cancer Institute Imaging Data Commons (IDC) https://portal.imaging.datacommons.cancer.gov/explore/



### Histology, Histopathology (H&E, IHQ) & Microscopy (Cell, Cytology, Biology, Protein, Molecular, Fluorescence)



* Pap Smear image database #1 ("SIPAKMed") https://www.cse.uoi.gr/~marina/sipakmed.html

* Pap Smear image database #2 https://www.cs.uoi.gr/~marina/data_set_TITB.zip

* Pap Smear image database #3 http://mde-lab.aegean.gr/index.php/downloads

* The Cancer Genome Atlas (TCGA) http://cancergenome.nih.gov/ https://tcga-data.nci.nih.gov/tcga/

* International Cancer Genome Consortium http://icgc.org, (Data portal) http://dcc.icgc.org/

* Stanford Tissue Microarray Database (TMA) http://tma.im

* MITOS dataset http://www.ipal.cnrs.fr/event/icpr-2012

* DPA’s Whole Slide Imaging Repository https://digitalpathologyassociation.org/whole-slide-imaging-repository

* ITK Analysis of Large Histology Datasets http://www.na-mic.org/Wiki/index.php/ITK_Analysis_of_Large_Histology_Datasets

* Histology Photo Album http://www.histology-world.com/photoalbum/thumbnails.php?album=52

* Slide Library of Virtual pathology, University of Leeds http://www.virtualpathology.leeds.ac.uk/

* BDGP images from the FlyExpress database www.flyexpress.net

* The UCSB Bio-Segmentation Benchmark dataset http://www.bioimage.ucsb.edu/research/biosegmentation

* Histology (CIMA) dataset http://cmp.felk.cvut.cz/~borovji3/?page=dataset

* ANHIR dataset https://anhir.grand-challenge.org/

* Genome RNAi dataset http://www.genomernai.org/

* Chinese Hamster Ovary cells (CHO) dataset http://www.chogenome.org/data.html

* Allen Brain Atlas http://www.brain-map.org/

* 1000 Functional Connectomes Project http://fcon_1000.projects.nitrc.org/

* The Cell Centered Database (CCDB) https://library.ucsd.edu/dc/collection/bb5940732k

* The Encyclopedia of DNA Elements (ENCODE) http://genome.ucsc.edu/ENCODE/ 

user guide: http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001046

* The Human Protein Atlas: http://www.proteinatlas.org/

* El Salvador Atlas of Gastrointestinal VideoEndoscopy Images and Videos of hi-res of studies taken from Gastrointestinal Video endoscopy http://www.gastrointestinalatlas.com/

* BCNB: Early Breast Cancer Core-Needle Biopsy WSI Dataset, https://bupt-ai-cz.github.io/BCNB/, https://github.com/bupt-ai-cz/BALNMP#bcnb-dataset

* BCI: Breast Cancer Immunohistochemical Image Generation Dataset, https://bupt-ai-cz.github.io/BCI/, https://github.com/bupt-ai-cz/BCI



### Databases you can use for benchmarking 



* http://peipa.essex.ac.uk/benchmark/databases/

* http://mulan.sourceforge.net/datasets-mlc.html

* Datasets reporting formats for pathologists http://www.rcpath.org/publications-media/publications/datasets



### State of the art / Challenges



* Grand Challenges in Medical Image Analysis https://grand-challenge.org/

* Challenges in global health and development problems https://grandchallenges.org/#/map

* Current state of the art of most used computer vision datasets: Who is the best at X? http://rodrigob.github.io/are_we_there_yet/build/

* Automatic Non-rigid Histological Image Registration (ANHIR) challenge https://anhir.grand-challenge.org/