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

Image Datasets

• 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/
• Grand Challenges in Medical Image Analysis http://www.grand-challenge.org/index.php/Main_Page

Multimodal databases

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

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

• The Histology Image Dataset (histologyDS) http://www.informed.unal.edu.co/histologyDS
• 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://ipal.cnrs.fr/ICPR2012/
• Cancer Image Database (caIMAGE) http://cancerim ages.nci.nih.gov/caIMAGE/
• DPA’s Whole Slide Imaging Repository https://digitalpathologyassociation.org/whole-slide-imaging-repository
• Atlas of bleast Histology http://www.webmicroscope.net/atlases/breast/brcatlas_start.asp
• 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/
• Tissue Acquisition and Banking Services (TABS) of the NYU Experimental Pathology Core Facilities http://pathology.med.nyu.edu/research/core-laboratories/tissue-banking
• Aperio Images http://images2.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://labs.fme.aegean.gr/decision/downloads
• BIICBU Biological Image Repository http://ome.grc.nia.nih.gov/iicbu2008/
• RNAi dataset http://ome.grc.nia.nih.gov/iicbu2008/rnai/index.html
• Chinese Hamster Ovary cells (CHO) dataset http://ome.grc.nia.nih.gov/iicbu2008/hela/index.html#cho
• Locate Endogenus mouse sub-cellular organelles (END) databaset http://locate.imb.uq.edu.au/
• 2D HeLa dataset (HeLa) datgaset http://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) http://ccdb.ucsd.edu/index.shtm
• The Encyclopedia of DNA Elements (ENCODE) http://genome.ucsc.edu/ENCODE/
• 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
• http://www.dmoz.org/Computers/Artificial_Intelligence/Machine_Learning/Datasets/
• Benchmark Data Sets for Highly Imbalanced Binary Classification http://www.cs.gsu.edu/~zding/research/benchmark-data.php
• 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/