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

A list of Medical imaging datasets.

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

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A list of Medical imaging datasets.

https://github.com/camlloyd/medical-imaging-datasets/blob/master/

# 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)
* Alzheimers 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

### Histology and Histopathology (H&E, IHQ, ...)

* 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
* Cancer Image Database (caIMAGE) https://emice.nci.nih.gov/caimage
* DPAs 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/
* Aperio Images http://images.aperio.com/
* HAPS Histology Image Database http://hapshistology.wikifoundry.com/
* Microscopy (Cell, Cytology, Biology, Protein, Molecular, Fluorescence, etc.)
* BDGP images from the FlyExpress database www.flyexpress.net
* The UCSB Bio-Segmentation Benchmark dataset http://www.bioimage.ucsb.edu/research/biosegmentation
* Pap Smear database http://mde-lab.aegean.gr/index.php/downloads


* Genome RNAi dataset http://www.genomernai.org/
* Chinese Hamster Ovary cells (CHO) dataset http://www.chogenome.org/data.html
* Locate Endogenus mouse sub-cellular organelles (END) databaset http://locate.imb.uq.edu.au/
* 2D HeLa dataset (HeLa) dataset https://ome.grc.nia.nih.gov/iicbu2008/hela/index.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/
* DRIVE: Digital Retinal Images for Vessel Extraction http://www.isi.uu.nl/Research/Databases/DRIVE/ (Ground truth)
* El Salvador Atlas of Gastrointestinal VideoEndoscopy Images and Videos of his-res of studies taken from Gastrointestinal Video endoscopy http://www.gastrointestinalatlas.com/

### Databases you can use for bechmarking 

* http://peipa.essex.ac.uk/benchmark/databases/
* http://mulan.sourceforge.net/datasets-mlc.html
* https://archive.ics.uci.edu/ml/datasets.html
* Datasets reporting formats for pathologists http://www.rcpath.org/publications-media/publications/datasets
* DermNet - Skin disease atlas (23 image classes and 23,000 images): http://www.dermnet.com/

### 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/

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