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  1. Kaur T, Saini BS, Gupta S. A joint intensity and edge magnitude-based multilevel thresholding algorithm for the automatic segmentation of pathological MR brain images. Neural Computing and Applications. 2016:1-24. doi: 10.1007/s00521-016-2751-4

  2. Song J, Liu Z, Zhong W, Huang Y, Ma Z, Dong D, Liang C, Tian J. Non-small cell lung cancer: quantitative phenotypic analysis of CT images as a potential marker of prognosis. Scientific reports. 2016;6:38282:1-9. doi: 10.1038/srep38282

  3. Crawford L, Monod A, Chen AX, Mukherjee S, Rabadán R. Topological Summaries of Tumor Images Improve Prediction of Disease Free Survival in Glioblastoma Multiforme. arXiv preprint arXiv:161106818. 2016:1-29.

  4. Korfiatis P, Kline TL, Erickson BJ. Automated Segmentation of Hyperintense Regions in FLAIR MRI Using Deep Learning. J Tomography, 2016, 2:4(334-340) DOI: 10.18383/j.tom.2016.00166
  5. Zheng C, Wang X, Feng D, editors. Topology guided demons registration with local rigidity preservation. Engineering in Medicine and Biology Society (EMBC), 2016 IEEE 38th Annual International Conference; 2016: IEEE.

  6. Kotrotsou A, Zinn PO, Colen RR. Radiomics in Brain Tumors: An Emerging Technique for Characterization of Tumor Environment. Magnetic Resonance Imaging Clinics of North America. 2016;24(4):719-29.

  7. Zhao B, Tan Y, Tsai WY, Qi J et al. Reproducibility of radiomics for deciphering tumor phenotype with imaging. Sci Rep. 2016 Mar 24;6:23428. (link)
  8. Li H, Zhu Y, Burnside ES, Huang E, et al. Quantitative MRI radiomics in the prediction of molecular classifications of breast cancer subtypes in the TCGA/TCIA data set. npj Breast Cancer (2016). (link)
  9. Grossmann P, Gutman DA, et al. Imaging-genomics reveals driving pathways of MRI derived volumetric tumor phenotype features in Glioblastoma. BMC Cancer (2016). (link)
  10. Zhu Y, Li H, Guo W, Drukker K, et al. Deciphering Genomic Underpinnings of Quantitative MRI-based Radiomic Phenotypes of Invasive Breast Carcinoma. Sci Rep (2015). (link) 
  11. Rajakumar K, Muttan S, Deepa G, Revathy S, Priya BS. Intelligent texture feature extraction and indexing for MRI image retrieval using curvelet and PCA with HTF. Advances in Natural and Applied Sciences. 2015 Jun 1;9(6 SE):506-13. (link)
  12. Parmar, C., R. T. Leijenaar, et al. (2015). "Radiomic feature clusters and Prognostic Signatures specific for Lung and Head &Neck cancer." Sci Rep 5: 11044.

  13.  Parmar, C., P. Grossmann, et al. (2015). "Machine Learning methods for Quantitative Radiomic Biomarkers." Sci Rep 5: 13087.
  14. Tanougast C, Chaddad A. High-Throughput Quantification of Phenotype Heterogeneity Using Statistical Features. Adv Bioinformatics (2015). (link)
  15. Chaddad A. Automated Feature Extraction in Brain Tumor by Magnetic Resonance Imaging Using Gaussian Mixture Models.  International Journal of Biomedical Imaging, 2015. (link)
  16. Dhara AK, Mukhopadhyay S, Khandelwal N. 3d texture analysis of solitary pulmonary nodules using co-occurrence matrix from volumetric lung CT images. SPIE 2013. (link)
  17. Dhara AK, Mukhopadhyay S, Alam N, Khandelwal N. Measurement of spiculation index in 3D for solitary pulmonary nodules in volumetric lung CT images. Proc. SPIE 8670, Medical Imaging 2013: Computer-Aided Diagnosis, 86700K. (link)

Algorithm Development

  1. Hsieh KL-C, Tsai R-J, Teng Y-C, Lo C-M. Effect of a computer-aided diagnosis system on radiologists' performance in grading gliomas with MRI. PloS one. 2017;12(2):e0171342 (link)

  2. Hsieh KL-C, Lo C-M, Hsiao C-J. Computer-aided grading of gliomas based on local and global MRI features. Computer Methods and Programs in Biomedicine. 2017;139:31-8. (link)

  3. Yang H, Liu F, Wang Z, Tang H, Sun S, Sun S. Research on the Content-Based Classification of Medical Image. Journal of Medical Imaging and Health Informatics. 2017;7(1):129-36. (link)

  4. Rezaie AA, Habiboghli A. Detection of Lung Nodules on Medical Images by the Use of Fractal Segmentation. International Journal of Interactive Multimedia and Artificial Inteligence. 2017;4(Special Issue on 3D Medicine and Artificial Intelligence):15-9. (link)

  5. Chen H, Zhang Y, Zhang W, Liao P, Li K, Zhou J, Wang G. Low-dose CT via convolutional neural network. Biomedical Optics Express. 2017;8(2):679-94.(link)

  6. Vallières M, Freeman C, Skamene S, El Naqa I. A radiomics model from joint FDG-PET and MRI texture features for the prediction of lung metastases in soft-tissue sarcomas of the extremities. Physics in medicine and biology. 2015;60(14):5471.
  7. Kazdal S, Dogan B, Camurcu AY, editors. Computer-aided detection of brain tumors using image processing techniques. Signal Processing and Communications Applications Conference (SIU), 2015 23th; 2015: IEEE.
  8. Gupta A, Martens O, Le Moullec Y, Saar T, editors. A tool for lung nodules analysis based on segmentation and morphological operation. Intelligent Signal Processing (WISP), 2015 IEEE 9th International Symposium on; 2015: IEEE.
  9. Benninghoff H, Garcke H. Segmentation of Three-dimensional Images with Parametric Active Surfaces and Topology Changes. arXiv preprint arXiv:150607136. 2015.
  10. Zabala-Travers S, Choi M, Cheng W-C, Badano A. Effect of color visualization and display hardware on the visual assessment of pseudocolor medical images. Medical Physics. 2015;42(6):2942-54.
  12. Grove O, Berglund AE, Schabath MB, Aerts HJ, Dekker A, Wang H, Velazquez ER, Lambin P, Gu Y, Balagurunathan Y. Quantitative Computed Tomographic Descriptors Associate Tumor Shape Complexity and Intratumor Heterogeneity with Prognosis in Lung Adenocarcinoma. PloS one. 2015;10(3).
  13. Buerger C, Sénégas J, Kabus S, Carolus H, Schulz H, Agarwal H, Turkbey B, Choyke P, Renisch S. Comparing nonrigid registration techniques for motion corrected MR prostate diffusion imaging. Medical physics. 2015;42(1):69-80.
  14. Abedini M, Codella N, Connell J, Garnavi R, Merler M, Pankanti S, Smith J, Syeda-Mahmood T. A generalized framework for medical image classification and recognition. IBM Journal of Research and Development. 2015;59(2/3):1: -: 18.
  15. Blessy SPS, Sulochana CH. Performance analysis of unsupervised optimal fuzzy clustering algorithm for MRI brain tumor segmentation. Technology and Health Care. 2014.
  16. ElNawasany AM, Ali AF, Waheed ME. A Novel Hybrid Perceptron Neural Network Algorithm for Classifying Breast MRI Tumors.  Advanced Machine Learning Technologies and Applications: Springer; 2014. p. 357-66.
  17. Hong S, Huang Y, Cao Y, Chen X, Han J-DJ. Approaches to uncovering cancer diagnostic and prognostic molecular signatures. Molecular & Cellular Oncology. 2014.
  18. Codella N, Connell J, Pankanti S, Merler M, and Smith JR. Automated Medical Image Modality Recognition by Fusion of Visual and Text Information. Medical Image Computing and Computer-Assisted Intervention. 2014, Springer. 487-495. (link)
  19. Ertugrul OF. Adaptive Texture Energy Measure Method. International Journal of Intelligent Information Systems. 2014. 3(2):13-18. doi:10.11648/j.ijiis.20140302.11 (link)
  20. Kawa J, Juszczyk J, Pyciński B, Badura P, Pietka E. Radiological Atlas for Patient Specific Model Generation. Information Technologies in Biomedicine, 2014 4:69-82. 10.1007/978-3-319-06596-0_7. (link)
  21. Kowalik-Urbaniak I, Brunet D, Wang J, Koff D, Smolarski-Koff N, Vrscay ER, Wallace B, Wang Z.The quest for ‘diagnostically lossless’ medical image compression: a comparative study of objective quality metrics for compressed medical images. SPIE Medical Imaging. 2014. Vol. 9073. International Society for Optics and Photonics. doi:10.1117/12.2043196 (link)
  22. Naresh P and Shettar R. Image Processing and Classification Techniques for Early Detection of Lung Cancer for Preventive Health Care: A Survey. International Journal of Recent Trends in Engineering & Technology, 2014. 11:595-601 (link)
  23. Patel NP, Parmar SK, and Jain KR. Swift Pre Rendering Volumetric Visualization of Magnetic Resonance Cardiac Images based on Isosurface Technique. Procedia Technology, 2014. 14:422-429. doi:10.1016/j.protcy.2014.08.054 (link)
  24. Roy S, Brown MS, and Shih GL. Visual Interpretation with Three-Dimensional Annotations (VITA): Three-Dimensional Image Interpretation Tool for Radiological Reporting. Journal of Digital Imaging, 2014. 27(1):49-57. doi: 10.1007/s10278-013-9624-5 (link)
  25. Roth HR, Lu L, Seff A, Cherry KM, Hoffman J, Wang S, Liu J, Turkbey E, Summers RM. A new 2.5 D representation for lymph node detection using random sets of deep convolutional neural network observations.  Medical Image Computing and Computer-Assisted Intervention–MICCAI 2014: Springer; 2014. p. 520-7.

  26. Sivakumar S, and Chandrasekar C. A Study on Image Denoising for Lung CT Scan Images.International Journal of Emerging Technologies in Computational and Applied Sciences, 2014. 7(1):86-91 (link)
  27. Seff A, Lu L, Cherry KM, Roth HR, Liu J, Wang S, Hoffman J, Turkbey EB, Summers RM. 2d view aggregation for lymph node detection using a shallow hierarchy of linear classifiers.  Medical Image Computing and Computer-Assisted Intervention–MICCAI 2014: Springer; 2014. p. 544-52.

  28. Harmon S, Wendelberger B, and Jeraj R. SU-E-J-98: Radiogenomics: Correspondence Between Imaging and Genetic Features Based On Clustering Analysis. Medical Physics, 2014. 41(6): p. 178-178. doi:10.1118/1.4888150 (link)
  29. Krishnakumar V. and Parthiban L. Performance Analysis of Denoising in MR Images with Double Density Dual Tree Complex Wavelets, Curvelets and NonSubsampled Contourlet Transforms. Annual Review & Research in Biology, 2014. 4(19):2938-2956. doi:10.9734/ARRB/2014/9131#sthash.qFePVdL1.dpuf (link)
  30. Codella N, Merler M. IBM TJ Watson Research Center. Semantic Model Vector for ImageCLEF2013. June 18, 2014. (link)
  31. Agostinelli F, Anderson MR, and Lee H. Adaptive Multi-Column Deep Neural Networks with Application to Robust Image Denoising. Advances in Neural Information Processing Systems. 2013. (link)
  32. Agostinelli F, Anderson MR, Lee H, editors. Robust Image Denoising with Multi-Column Deep Neural Networks. Advances in Neural Information Processing Systems; 2013.

  33. Breseman K, Lee C, Bloch BN, and Jaffe C. Constructing 3D-Printable CAD Models of Prostates from MR Images. Bioengineering Conference (NEBEC),
    39th Annual Northeast , IEEE, 27-28. 5-7 April 2013. doi:10.1109/NEBEC.2013.8
  34. Buckler A, Liu TT, Savig E, Suzek BE, Rubin DL, and Paik D. Quantitative Imaging Biomarker Ontology (QIBO) for Knowledge Representation of Biomedical Imaging Biomarkers. Journal of Digital Imaging, 2013. 26(4):630-641. doi:10.1007/s10278-013-9599-2 (link)
  35. Heyns M, Breseman K, Lee C, Bloch BN, Jaffe C, and Xiang H. Design of a Patient-Specific Radiotherapy Treatment Target. Bioengineering Conference (NEBEC), 2013 39th Annual Northeast. 2013.171-172. IEEE.doi:10.1109/NEBEC.2013.75
  36. Kumar A, Kim J, Cai W, Fulham M, and Feng D. Content-Based Medical Image Retrieval: A Survey of Applications to Multidimensional and Multimodality Data. Journal of Digital Imaging, 2013. 26(6):1025-1039. doi: 10.1007/s10278-013-9619-2.(link)
  37. Lundström C. vPSNR: a visualization-aware image fidelity metric tailored for diagnostic imaging. International Journal of Computer Assisted Radiology and Surgery, 2013. 8(3):437-450. doi: 10.1007/s11548-012-0792-4 (link)
  38. Olmedo I, Guerra Perez Y, Johnson JF, Raut L, Hoe DHK. Image segmentation on GPGPUs: a cellular automata-based approach. Proceedings of the 2013 Summer Computer Simulation Conference. Society for Modeling & Simulation International. 2013. 51. (link)
  39. Pambrun JF, Noumeir R. Compressibility variations of JPEG2000 compressed computed tomography. Conference Proceedings, 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2013:3375-3378. doi: 10.1109/EMBC.2013.6610265 (link)
  40. Roozgard A, Barzigar N, Verma P, and Cheng S. 3D medical image denoising using 3D block matching and low-rank matrix completion. Signals, Systems and Computers, Asilomar Conference, 3-6 Nov. 2013, 253 – 257 IEEE. doi:10.1109/ACSSC.2013.6810271
  41. Yankeelov TE, Atuegwu N, Hormuth D, et al. Clinically Relevant Modeling of Tumor Growth and Treatment Response. Sci Transl Med. 2013 May 29;5(187):187ps9 doi: 10.1126/scitranslmed.3005686 (link) .
  42. Huang LC, Yseng LY, Hwang MS. A reversible data hiding method by histogram shifting in high quality medical images. Journal of Systems and Software 2013 March;86(3):716-27 doi: 10.1016/j.jss.2012.11.024 (link)
  43. Pheng HS and Shamsuddin SM. Texture classification of lung computed tomography images. 2012 International Conference on Graphic and Image Processing. 2013. Vol. 8768. International Society for Optics and Photonics. doi:10.1117/12.2011108 (link)
  44. Barzigar N, Roozgard A, Verma P, Cheng S. Removing Mixture Noise from Medical Images Using Block Matching Filtering and Low-Rank Matrix Completion. Healthcare Informatics, Imaging and Systems Biology, IEEE International Conference. 2012.134. doi:10.1109/HISB.2012.59 (link)
  45. Otake Y, Schafer S, Stayman JW, Zbijewski W, Kleinszig G, Graumann R, Khanna AJ, Siewerdsen JH. Automatic localization of target vertebrae in spine surgery using fast CT-to-fluoroscopy (3D-2D) image registration. SPIE Medical Imaging, 2012. Volume: 8316. International Society for Optics and Photonics. doi:10.1117/12.911308 (link)
  46. Roozgard A, Cheng AS, Liu H. Malignant nodule detection on lung ct scan images with kernel rx-algorithm. Biomedical and Health Informatics (BHI), 2012 IEEE-EMBS International Conference on 5-7 Jan. 2012 499 – 502. IEEE. doi: 10.1109/BHI.2012.6211627.
  47. Biancardi AM, Jirapatnakul AC, Reeves AP. A comparison of ground truth estimation methods. International Journal of Computer Assisted Radiology and Surgery, 2010. 5(3):295-305. doi: 10.1007/s11548-009-0401-3 (link)
  48. Soysal OM, Chen P, Schneider H. An Image Processing Tool for Efficient Feature Extraction in Computer-Aided Detection Systems. Granular Computing (GrC) IEEE International Conference 2010. 14-16 Aug. 438-442. doi:10.1109/GrC.2010.128
  49. Tseng LY and Huang LC. Automatic fissure detection in CT images based on the genetic algorithm. Machine Learning and Cybernetics (ICMLC), International Conference. IEEE. 2010. 5: 2583 – 2588. doi: 10.1109/ICMLC.2010.5580871
  50. Kumar, D., A. Wong, et al. (2015). Lung Nodule Classification Using Deep Features in CT Images. Computer and Robot Vision (CRV), 2015 12th Conference on, IEEE.

  51. Kanas, V. G., E. I. Zacharaki, et al. (2015). "A low cost approach for brain tumor segmentation based on intensity modeling and 3D Random Walker." Biomedical Signal Processing and Control 22: 19-30.

  52. Magdy, E., N. Zayed, et al. (2015). "Automatic Classification of Normal and Cancer Lung CT Images Using Multiscale AM-FM Features." International Journal of Biomedical Imaging 2015.

  53. Zayed, N. and H. A. Elnemr (2015). "Statistical Analysis of Haralick Texture Features to Discriminate Lung Abnormalities." International Journal of Biomedical Imaging 2015.

  54. Chaddad, A. and C. Tanougast "High-Throughput Quantification of Phenotype Heterogeneity Using Statistical Features." Advances in Bioinformatics 2015.  doi: 10.1155/2015/728164 
  55. Li M, Miller K, Joldes GR, Kikinis R, Wittek A. Biomechanical model for computing deformations for whole-body image registration: A meshless approach. International Journal for Numerical Methods in Biomedical Engineering. 2016. doi: 10.1002/cnm.2771


  1. Aerts HJ, Velazquez ER, et al. (2014). Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach. TCIA. Saint Louis, MO. (link)
  2. Armato SG and Drukker K, et al. (2015). SPIE-AAPM-NCI Lung Nodule Classification Challenge Dataset. TCIA. Saint Louis, MO. (link)
  3. Bloch N, Rusu M, et al. (2015) NCI-ISBI 2013 Challenge: Automated Segmentation of Prostate Structures. TCIA. St. Louis, MO. (link)
  4. Colen RR, Wang J, et al. (2014). Glioblastoma: Imaging Genomic Mapping Reveals Sex-specific Oncogenic Associations of Cell Death. TCIA. Saint Louis, MO. (link)
  5. Gevaert O, Mitchell LA, et al. (2014). Glioblastoma multiforme: exploratory radiogenomic analysis by using quantitative image features. TCIA. Saint Louis, MO. (link)

  6. Gevaert O, Xu J, et al. (2014). Non-small cell lung cancer: identifying prognostic imaging biomarkers by leveraging public gene expression microarray data--methods and preliminary results. TCIA. Saint Louis, MO. (link)
  7. Grove O, Berglund AE, et al. (2015). Data from: Quantitative computed tomographic descriptors associate tumor shape complexity and intratumor heterogeneity with prognosis in lung adenocarcinoma. TCIA. Saint Louis. MO. (link)
  8. Gutman DA, Cooper LA, et al. (2014). MR Imaging Predictors of Molecular Profile and Survival: Multi-institutional Study of the TCGA Glioblastoma Data Set. TCIA. Saint Louis, MO. (link)

  9. Huang W, Li X, et al. (2014). Variations of dynamic contrast-enhanced magnetic resonance imaging in evaluation of breast cancer therapy response: a multicenter data analysis challenge. TCIA. Saint Louis, MO. (link)

  10. Jain R, Poisson LM, et al. (2014). Outcome Prediction in Patients with Glioblastoma by Using Imaging, Clinical, and Genomic Biomarkers: Focus on the Nonenhancing Component of the Tumor. TCIA. Saint Louis, MO. (link)

  11. Kalpathy-Cramer J, Napel S, et al. (2015). QIN multi-site collection of Lung CT data with Nodule Segmentations. TCIA. Saint Louis, MO. (link)

  12. Lee J, Narang S, et al. (2015). Spatial Habitat Features derived from Multiparametric Magnetic Resonance Imaging data from Glioblastoma Multiforme cases. TCIA. Saint Louis, MO. (link)
  13. Liu F,  Hernandez-Cabronero M, et al. (2016). Image Data Used in the Simulations of "The Role of Image Compression Standards in Medical Imaging: Current Status and Future Trends". TCIA. Saint Louis, MO. (link 
  14. Mazurowski MA, Zhang J, et al. (2014). Radiogenomic Analysis of Breast Cancer: Luminal B Molecular Subtype Is Associated with Enhancement Dynamics at MR Imaging. TCIA. Saint Louis, MO. (link)
  15. Messay T, Hardie RC, et al. (2014). Segmentation of Pulmonary Nodules in Computed Tomography Using a Regression Neural Network Approach and its Application to the Lung Image Database Consortium and Image Database Resource Initiative Dataset. TCIA. Saint Louis, MO. (link)

  16. Morris E, Burnside M, et al. (2014). TCGA Breast Phenotype Research Group Data sets. TCIA. Saint Louis, MO (link)
  17. Roth H, Lu L, et al. (2015). A new 2.5D representation for lymph node detection in CT. TCIA. Saint Louis, MO. (link)

  18. Shinagare AB, Vikram R, et al. (2015). Radiogenomics of Clear Cell Renal Cell Carcinoma: Preliminary Findings of The Cancer Genome Atlas-Renal Cell Carcinoma (TCGA-RCC) Research Group. TCIA. Saint Louis, MO. (link)

  19. Vallières M, Freeman CR, et al. (2015). Data from: A radiomics model from joint FDG-PET and MRI texture features for the prediction of lung metastases in soft-tissue sarcomas of the extremities. TCIA. Saint Louis, MO. (link)


  1. Farahani K, Kalpathy-Cramer J, Chenevert TL, Rubin DL, Sunderland JJ, Nordstrom RJ, Buatti J, Hylton N. Computational Challenges and Collaborative Projects in the NCI Quantitative Imaging Network. Tomography: a journal for imaging research. 2016;2(4):242-9. (link)

  2. Kalpathy-Cramer J, Mamomov A, Zhao B, Lu L, Cherezov D, Napel S, Echegaray S, Rubin D, McNitt-Gray M, Lo P. Radiomics of Lung Nodules: A Multi-Institutional Study of Robustness and Agreement of Quantitative Imaging Features. Tomography: a journal for
    imaging research. 2016;2(4):430-7. doi:

  3. Clarke, L. P., R. J. Nordstrom, et al. (2014). "The Quantitative Imaging Network: NCI's Historical Perspective and Planned Goals." Translational Oncology 7(1): 1-4. (link)

  4. Huang, W., X. Li, et al. (2014). "Variations of dynamic contrast-enhanced magnetic resonance imaging in evaluation of breast cancer therapy response: a multicenter data analysis challenge." Transl Oncol 7(1): 153-166.

  5. Kalpathy-Cramer, J., J. B. Freymann, et al. (2014). "Quantitative Imaging Network: Data Sharing and Competitive AlgorithmValidation Leveraging The Cancer Imaging Archive." Translational oncology 7(1): 147-152.

  6. Levy, M. A., J. B. Freymann, et al. (2012). "Informatics methods to enable sharing of quantitative imaging research data." Magnetic Resonance Imaging.


Collection: CT Colonography

  1. Pang S, Yu Z, Orgun MA. A Novel End-to-End Classifier Using Domain Transferred Deep Convolutional Neural Networks for Biomedical Images. Computer Methods and Programs in Biomedicine. 2017. (link)
  2. Yahya-Zoubir B, Hamami L. et al. Automatic 3D Mesh-Based Centerline Extraction from a Tubular Geometry Form. Information Technology and Control, 2016. 45(2):156-163. (link)
  3. Alazmani A, Hood A, et al. Quantitative Assessment of Colorectal Morphology: Implications for Robotic Colonoscopy. Medical Engineering and Physics, 2016. 38(2):148-154. (link)
  4. Gayathri Devi K, Radhakrishnan R. Automatic Segmentation of Colon in 3D CT Images and Removal of Opacified Fluid Using Cascade Feed Forward Neural Network. Computational and Mathematical Methods in Medicine. 2015;2015.
  5. Namías R, et al., Automatic rectum limit detection by anatomical markers correlation. Computerized Medical Imaging and Graphics, 2014. 38(4):245-250.(link)
  6. Boone DJ, Halligan S, Roth HR, et al., CT Colonography: External Clinical Validation of an Algorithm for Computer-assisted Prone and Supine Registration. Radiology, 2013. 268(3):752-760.(link)
  7. Roth HR, et al., External clinical validation of prone and supine CT colonography registration in Abdominal Imaging. Computational and Clinical Applications 2012, Springer. 7601:10-19.(link)


titleThese refer to the Mouse-Mammary Collection data, created before submission to TCIA
  1. Jansen SA et al, NMR Biomed. 2011 Aug;24(7):880-7. 
  2. Jansen SA et al, Breast Cancer Res. 2009;11(5):R65. 
  3. Jansen SA et al, Radiology. 2009 Nov;253(2):399-406.
  4. Jansen SA et al, Phys Med Biol. 2008 Oct 7;53(19):5481-93.
  5. Jansen SA., Ductile carcinoma in situ: magnetic resonance and ultrasound imaging in mouse models of breast cancer (Mouse.Mammary.MRI.Ultrasound.Summary.pdf).
  6. Jansen S., Investigating genetic events in the progression of ductal carcinoma in situ (Mouse.Mammary.Genetics.DCIS.pdf).


Collection: NLST

Please see List of NLST Publications at NIH to browse publications from this Data Collection.

Collection: NSCLC-Radiomics

  1. Patil R, Mahadevaiah G, Dekker A. An Approach Toward Automatic Classification of Tumor Histopathology of Non–Small Cell Lung Cancer Based on Radiomic Features. Tomography: a journal for imaging research. 2016;2(4):374-7. (link)



Collection: Phantom FDA

  1. Peskin AP, Dima AA, Saiprasad G. An Automated Method for Locating Phantom modules in Anthropomorphic Thoracic Phantom CT Studies. The 2012 International Conference on Image Processing, Computer Vision, and Pattern Recognition. 2012.(link)
  2. Gavrielides MA, Kinnard LM, Myers KJ ,Peregoy J, Pritchard WF, Zeng R, Esparza J, Karanian J, Petrick N, A resource for the assessment of lung nodule size estimation methods: database of thoracic CT scans of an anthropomorphic phantom, Optics Express , vol. 18, n.14, pp. 15244-15255, 2010. (link)


titleThese refer to the QIN-Breast Collection data, created before submission to TCIA
  1. Li X, Dawant BM, Welch EB, Chakravarthy AB, Freehardt D, Mayer I, Kelley M, Meszoely I, Gore JC, Yankeelov TE. Validation of an algorithm for the nonrigid registration of longitudinal breast MR images using realistic phantoms. Medical Physics, 2010; 37:2541-52. PMCID: PMC2881925
  2. Atuegwa NC, Gore JC, Yankeelov TE. Using Quantitative Imaging Data to Drive Mathematical Models of Tumor Growth and Treatment Response. Physics in Medicine and Biology, 2010; 55:2429-49. PMCID: PMC2897238
  3. Yankeelov TE, Arlinghaus L, Li X, Gore JC. The role of magnetic resonance imaging biomarkers in clinical trials of treatment response in cancer. Seminars in Oncology, 2011; 38:16-25. PMCID: PMC3073543
  4. Arlinghaus L, Li X, Levy M, Smith D, Welch WB, Gore JC, Yankeelov TE. Current and Future Trends in Magnetic Resonance Imaging Assessments of the Response of Breast Tumors to Neoadjuvant Chemotherapy. Journal of Oncology, 2010. pii: 919620. Epub 2010 Sep 29. PMCID: PMC2952974
  5. Arlinghaus LR, Welch EB, Chakravarthy AB, Farley JS, Gore JC, Yankeelov TE. Motion and distortion correction in diffusion-weighted MRI of the breast at 3T. Journal of Magnetic Resonance Imaging, 2011; 33:1063-70. PMCID: PMC3081111
  6. Gore JC, Manning HC, Quarles CC, Waddell KW, Yankeelov TE. Magnetic Resonance in the Era of Molecular Imaging of Cancer. Magnetic Resonance Imaging, 2011; 29:587-600. PMCID: PMC3285504
  7. Arlinghaus LR, Li X, Rahman AR, Welch EB, Xu L, Gore JC, Yankeelov TE. On the Relationship Between the Apparent Diffusion Coefficient and Extravascular Extracellular Volume Fraction in Human Breast Cancer. Magnetic Resonance Imaging, 2011; 29:630-8. PMCID: PMC3100356
  8. Smith DS, Welch EB, Li X, Arlinghaus LD, Loveless ME, Koyama T, Gore JC, Yankeelov TE. Quantitative effects of accelerated dynamic contrast enhanced MRI data using compressed sensing. Physics in Medicine and Biology, 2011; 56:4933-46. PMCID: PMC3192434
  9. Li, X, Welch EB, Chakravarthy B, Mayer I, Meszeoly I, Kelley M, Means-Powell J, Gore JC, Yankeelov TE. A novel AIF tracking method and comparison of DCE-MRI parameters using individual and population-based AIFs in human breast cancer. Physics in Medicine and Biology, 2011; 56:5753-69. PMCID: PMC3176673


Collection: QIN Breast DCE-MRI

  1. Nowaková J, Prílepok M, Snášel V. Medical Image Retrieval Using Vector Quantization and Fuzzy S-tree. Journal of Medical Systems. 2017;41(2):18. (link)

Collection: QIN GBM DCE-MRI

  1. Gerstner ER, Zhang Z, Fink JR, Muzi M, Hanna L, Greco E, Mintz A, Kostakoglu L, Eikman EA, Prah MA, Ellingson BM, Ratai EM, Schmainda KM, Sorensen G, Barboriak DP,  Mankoff DA. ACRIN 6684: Assessment of tumor hypoxia in newly diagnosed GBM using 18F-FMISO PET and MRI. Clin Cancer Res 2016. Accepted.
  2. Gerstner ER, Zhang Z, Fink JR, Muzi M, Hanna L, Greco E, Mintz A, Kostakoglu L, Eikman EA, Prah M, Schmainda KM, Sorensen GA, Barboriak D,  Mankoff DA. ACRIN 6684: Assessment of tumor hypoxia in newly diagnosed GBM using 18F-FMISO PET and MRI. J Clin Oncol 33(Suppl):2024. 2015.
  3. Fink JR, Zhang Z, Gerstner ER, Muzi M, Kostakoglu L, Mintz A, Eikman EA, Barboriak D,  Mankoff DA. ACRIN 6684: Multicenter phase II assessment of tumor hypoxia in glioblastoma using 18F-Fluoromisonidazole (FMISO) PET and MRI. J Nucl Med 56(Suppl3):325. 2015.
  4. Fink JR, Muzi M, Peck M,  Krohn KA. Multimodality Brain Tumor Imaging: MR Imaging, PET, and PET/MR Imaging. J Nucl Med 56(10):1554-1561. 2015.
  5. Muzi M, Fink JR, Richards TL, Marro KI, Wong T, Muzi JP, Eary JF, Rockhill JK,  Krohn KA. Evaluation of PET and MR measurements to examine progression in glioma patients. J Nucl Med 55(Suppl1):1512-. 2014.


titleThese refer to the RIDER Collections data, created before submission to TCIA
  1. Meyer CR, Armato SG III, Fenimore CP, McLennan G, Bidaut LM, Barboriak DP, Gavrielides MA, Jackson EF, McNitt-Gray MF, Kinahan PE, Petrick N, Zhao B. Quantitative imaging to assess tumor response to therapy: Common themes of measurement, truth data and error sources. Translational Oncology 2: 198–210, 2009. (link)
  2. McNitt-Gray MF, Bidaut LM, Armato SG III, Meyer CR, Gavrielides MA, Fenimore CP, McLennan G, Petrick N, Zhao B, Reeves AP, Beichel R, Kim H-J, Kinnard L. CT assessment of response to therapy: Tumor volume change measurement, truth data and error.Translational Oncology2009. 2:216–222. (link)
  3. Kinahan PE, Doot RK, Wanner-Roybal M, Bidaut LM, Armato SG III, Meyer CR, McLennan G.PET/CT assessment of response to therapy: Tumor change measurement, truth data and error.Translational Oncology 2:223–230, 2009. (link)
  4. Jackson EF, Barboriak DP, Bidaut LM, Meyer CR. Magnetic resonance assessment of response to therapy: tumor change measurement, truth data and error sources.Translational Oncology 2009 Dec;2(4):211-5. PubMed PMID: 19956380; PubMed Central PMCID: PMC2781079. (link)
  5. Armato SG 3rd, Meyer CR, Mcnitt-Gray MF, McLennan G, Reeves AP, Croft BY, Clarke LP;RIDER Research Group. The Reference Image Database to Evaluate Response to therapy in lung cancer (RIDER) project: a resource for the development of change-analysis software.Clin Pharmacol Ther. 2008 Oct;84(4):448-56. PubMed PMID: 18754000. (link)


Collection: SPIE-AAPM Lung CT Challenge

  1. Nishio M, Nagashima C. Computer-aided Diagnosis for Lung Cancer: Usefulness of Nodule Heterogeneity. Academic Radiology. 2017;24(3):328-36. (link)

Collection: TCGA-BRCA

  1. Wu J, Cui Y, Sun X, Cao G, Li B, Ikeda DM, Kurian AW, Li R. Unsupervised clustering of quantitative image phenotypes reveals breast cancer subtypes with distinct prognoses and molecular pathways. Clinical Cancer Research. 2017:clincanres. 2415.016. (link)

  2. Mazurowski MA, Zhang J, Grimm LJ, Yoon SC, Silber JI. Radiogenomic Analysis of Breast Cancer: Luminal B Molecular Subtype Is Associated with Enhancement Dynamics at MR Imaging. Radiology, 2014. DOI: 10.1148/radiol.14132641 (link)
  3. Lavasani, S. N., A. F. Kazerooni, et al. (2015). Discrimination of Benign and Malignant Suspicious BreastTumors Based on Semi-Quantitative DCE-MRI ParametersEmploying Support Vector Machine. Frontiers in Biomedical Technologies 2(2): 397-403.

  4. Anand, S., V. Vinod, et al. Application of Fuzzy c-means and Neural networks to categorize tumor affected breast MR Images. International Journal of Applied Engineering Research 10(64): 2015.

  5. Guo, W., H. Li, et al. (2015). Prediction of clinical phenotypes in invasive breast carcinomas from the integration of radiomics and genomics data. Journal of Medical Imaging 2(4): 041007-041007.

Collection: TCGA-GBM

  1. Cui Y, Ren S, Tha KK, Wu J, Shirato H, Li R. Volume of high-risk intratumoral subregions at multi-parametric MR imaging predicts overall survival and complements molecular analysis of glioblastoma. European Radiology. 2017:1-10. (link)

  2. Kanas VG, Zacharaki EI, Thomas GA, Zinn PO, Megalooikonomou V, Colen RR. Learning MRI-based classification models for MGMT methylation status prediction in glioblastoma. Computer Methods and Programs in Biomedicine. 2017;140:249-57.(link)

  3. Czarnek N, Clark K, Peters KB, Mazurowski MA. Algorithmic three-dimensional analysis of tumor shape in MRI improves prognosis of survival in glioblastoma: a multi-institutional study. Journal of Neuro-Oncology. 2017:1-8. (link)

  4. Chaddad A, Desrosiers C, Toews M, editors. Radiomic analysis of multi-contrast brain MRI for the prediction of survival in patients with glioblastoma multiforme. Engineering in Medicine and Biology Society (EMBC), 2016 IEEE 38th Annual International Conference; 2016.

  5. Prasanna, P., Patel, J., Partovi, S. et al. Radiomic features from the peritumoral brain parenchyma on treatment-naïve multi-parametric MR imaging predict long versus short-term survival in glioblastoma multiforme: Preliminary findings.  Eur Radiol (2016) pp 1–10. DOI:10.1007/s00330-016-4637-3

  6. Mulvey M, Muhyadeen S,  Sinha U. Classification of Glioblastoma Multiforme Molecular Subtypes Using Three-Dimensional Multi-Modal MR Imaging Features. Med. Phys. 43, 3373 (2016); (link)

  7. Ren X, Cui Y, Gao H,  Li, R. Identifying High-Risk Tumor Volume Based On Multi-Region and Integrated Analysis of Multi-Parametric MR Images for Prognostication of Glioblastoma. Med. Phys. 43, 3751 (2016); (link)
  8. Dunn WD Jr,  Aerts HJWL, et al.  Assessing the Effects of Software Platforms on Volumetric Segmentation of Glioblastoma.   J   Neuroimaging Psychiatry Neurol 2016. 1(2): 64-72.
  9. Upadhaya T, Morvan Y, et al. Prognosis classification in glioblastoma multiforme using multimodal MRI derived heterogeneity textural features: impact of pre-processing choices. Proc. SPIE 9785, Medical Imaging 2016: Computer-Aided Diagnosis, 97850W (March 24, 2016); (link)
  10. Upadhaya T, Morvan Y, et al. Prognostic value of multimodal MRI tumor features in Glioblastoma multiforme using textural features analysis. In Biomedical Imaging (ISBI), 2015 IEEE 12th International Symposium on, pp. 50-54. IEEE, 2015.

  11. Upadhaya T, Morvan Y, et al. A framework for multimodal imaging-based prognostic model building: Preliminary study on multimodal MRI in Glioblastoma Multiforme. IRBM. 2015 Nov 30;36(6):345-50.

  12. Reza SM, Mays R, Iftekharuddin KM, editors. Multi-fractal detrended texture feature for brain tumor classification. SPIE Medical Imaging; 2015: International Society for Optics and Photonics.

  13. Nabizadeh N, Kubat M. Brain tumors detection and segmentation in MR images: Gabor wavelet vs. statistical features. Computers & Electrical Engineering. 2015.

  14. Natteshan N, Jothi JAA. Automatic Classification of Brain MRI Images Using SVM and Neural Network Classifiers.  Advances in Intelligent Informatics: Springer; 2015. p. 19-30. (link)

  15. Zhang J, Barboriak DP, Hobbs H, Mazurowski MA. A fully automatic extraction of magnetic resonance image features in Glioblastoma patients. Medical physics. 2014;41(4):042301.

  16. Wangaryattawanich P, Wang J, Thomas GA, Chaddad A, Zinn PO, Colen RR, editors. Survival analysis of pre-operative GBM patients by using quantitative image features. Control, Decision and Information Technologies (CoDIT), 2014 International Conference on; 2014: IEEE.

  17. Colen RR, Wang J, Singh SK, Gutman DA, Zinn PO. Glioblastoma: Imaging Genomic Mapping Reveals Sex-specific Oncogenic Associations of Cell Death. Radiology. 2014.

  18. Colen RR, Vangel M, Wang J, Gutman DA, Hwang SN, Wintermark M, Rajan J, Jilwan-Nicola M, Chen JY, Raghavan P, Holder CA, Rubin D, Huang E, Kirby J, Freymann J, Jaffee CC, Flanders A, Zinn PO. Imaging genomic mapping of an invasive MRI phenotype predicts patient outcome and metabolic dysfunction: a TCGA glioma phenotype research group project.BMC Medical Genomics, 2014. 7(1):30. DOI: 10.1186/1755-8794-7-30 (link)
  19. Gevaert O, Mitchell LA, Achrol AS, Xu J, Echegaray S, Steinberg GK, Chesier SH, Napel S, Zaharchuk G, Plevritis SK. Glioblastoma Multiforme: Exploratory Radiogenomic Analysis by Using Quantitative Image Features. Radiology, 2014. doi: 10.1148/radiol.14131731 (link)
  20. Mazurowski MA, Zhang J, Peters KB, and Hobbs H. Computer-extracted MR imaging features are associated with survival in glioblastoma patients. Journal of Neuro-Oncology, 2014. 120(3):483–488 DOI: 10.1007/s11060-014-1580-5 (link)
  21. Jain R, Poisson L, Gutman D, Scarpace L, Hwang SN, Holder C, Wintermark M, Colen RR, Kirby J, Freymann J, Jaffe C, Mikkelsen T, Flanders A. Outcome Prediction in Patients with Glioblastoma by Using Imaging, Clinical, and Genomic Biomarkers: Focus on the Nonenhancing Component of the Tumor. Radiology. 2014 Aug;272(2):484-93. doi: 10.1148/radiol.14131691. Epub 2014 Mar 19. 2014 (link)
  22. Nicolasjilwan M, Hu Y, Yan C, Meerzaman D, Holder CA, Gutman D, et al. Addition of MR imaging features and genetic biomarkers strengthens glioblastoma survival prediction in TCGA patients. Journal of Neuroradiology, July 2014. doi: 10.1016/j.neurad.2014.02.006

  25. Kwon D, Shinohara RT, Akbari H, Davatzikos C. Combining Generative Models for Multifocal Glioma Segmentation and Registration.  Medical Image Computing and Computer-Assisted Intervention–MICCAI 2014: Springer; 2014. p. 763-70.

  28. Gutman DA, Cooper LAD, Hwang SN, Holder CA, Gao J, Aurora TD, Dunn WD, Scarpace L, Mikkelsen T, Jain R, Wintermark M, Jilwan M, Raghavan P, Huang E, Clifford RJ, Monqkolwat P, Kleper V, Freymann J, Kirby J, Zinn PO, Moreno CS, Jaffe C, Colen R, Rubin DL, Saltz J, Flanders A, Brat DJ. MR Imaging Predictors of Molecular Profile and Survival: Multi-institutional Study of the TCGA Glioblastoma Data Set. Radiology. 2013 May:267(2):560-569,doi:10.1148/radiol.13120118 (link)
  29. Jain R, Poisson L, Narang J, Gutman D, Scarpace L, Hwang SN, Holder C, Wintermark M, Colen RR, Kirby J, Freymann J, Brat DJ, Jaffe C, Mikkelsen T. Genomic Mapping and Survival Prediction in Glioblastoma: Molecular Subclassification Strengthened by Hemodynamic Imaging Biomarkers. Radiology, 2013 Apr:267(1):212 –220, doi:10.1148/radiol.12120846 (link)
  30. Mazurowski MA, Desjardins A, Malof JM. Imaging descriptors improve the predictive power of survival models for glioblastoma patients. Neuro-oncology, 2013. 15(10):1389-1394 (link)
  31. Zinn PO, Colen RR. Imaging Genomic Mapping in Glioblastoma. Neurosurgery 60:126-130. Aug 2013 (link)
  32. Jain R, Poisson L, Narang J, Scarpace L, Rosenblum ML, Rempel S, Mikkelson T. Correlation of Perfusion Parameters with Genes Related to Angiogenesis Regulation in Glioblastoma: A Feasibility Study. American Journal of Neuroradiology, 2012. 33(7):1343-1348 [Epub ahead of print] (link)
  33. Zinn PO, Sathyan P, Mahajan B, Bruyere J, Hegi M, et al. A Novel Volume-Age-KPS (VAK) Glioblastoma Classification Identifies a Prognostic Cognate microRNA-Gene Signature. PLoS ONE, 2012 7(8): e41522. doi:10.1371/journal.pone.0041522 (link)
  34. Zinn PO, Majadan B, Sathyan P, Singh SK, Majumder S, et al. Radiogenomic Mapping of Edema/Cellular Invasion MRI-Phenotypes in Glioblastoma Multiforme. PLoS ONE, 2011 6(10): e25451. doi:10.1371/journal.pone.0025451 (link)
  35. Wangaryattawanich, P., M. Hatami, et al.  "Multicenter imaging outcomes study of The Cancer Genome Atlas glioblastoma patient cohort: imaging predictors of overall and progression-free survival." Neuro-oncology, (2015): nov117 .

  36. Kuo, J. S., K. B. Pointer, et al. (2015). "139 Human Ether-a-Go-Go-Related-1 Gene (hERG) K+ Channel as a Prognostic Marker and Therapeutic Target for Glioblastoma." Neurosurgery 62: 210-211.

  37. Zinn, P. O., M. Hatami, et al. (2015). "138 Diffusion MRI ADC Mapping of Glioblastoma Edema/Tumor Invasion and Associated Gene Signatures." Neurosurgery 62: 210.

  38. Steed, T., J. Treiber, et al. (2015). "Iterative Probabilistic Voxel Labeling: Automated Segmentation for Analysis of The Cancer Imaging Archive Glioblastoma Images." American Journal of Neuroradiology 36(4): 678-685.

  39. Lee, J., S. Narang, et al. (2015). "Associating spatial diversity features of radiologically defined tumor habitats with epidermal growth factor receptor driver status and 12-month survival in glioblastoma: methods and preliminary investigation." Journal of Medical Imaging 2(4): 041006-041006.

  40. Itakura, H., A. S. Achrol, et al. (2015). "Magnetic resonance image features identify glioblastoma phenotypic subtypes with distinct molecular pathway activities." Science Translational Medicine 7(303): 303ra138-303ra138.

  41. Cui, Y., K. K. Tha, et al. (2015). "Prognostic Imaging Biomarkers in Glioblastoma: Development and Independent Validation on the Basis of Multiregion and Quantitative Analysis of MR Images." Radiology: 150358.

  42. Lee, J., S. Narang, et al. (2015). "Spatial Habitat Features Derived from Multiparametric Magnetic Resonance Imaging Data Are Associated with Molecular Subtype and 12-Month Survival Status in Glioblastoma Multiforme." PloS one 10(9): e0136557.

  43. Rios Velazquez E, Meier R, Dunn WD Jr, Alexander B, Wiest R, Bauer S, Gutman DA, Reyes M, Aerts HJ. "Fully automatic GBM segmentation in the TCGA-GBM dataset: Prognosis and correlation with VASARI features." Sci Rep. 2015 Nov 18;5:16822. doi: 10.1038/srep16822.

Collection: TCGA-KIRC 

  1. Chen X, Zhou Z, Thomas K, Wang J. Predicting Gene Mutations in Renal Cell Carcinoma Based On CT Imaging Features: Validation Using TCGA-TCIA Datasets. Med. Phys. 43, 3705 (2016); (link)
  2. Zhu H, Chen H, Lin Z, Shi G, Lin X, Wu Z, Zhang X. Identifying molecular genetic features and oncogenic pathways of clear cell renal cell carcinoma through the anatomical (PADUA) scoring system. Oncotarget. 2016. (link)
  3. Shinagare AB, Vikram R, Jaffe C, Akin O, Kirby J, Huang E, Freymann J, Sainani NI, Sadow CA, Bathala TK. Radiogenomics of clear cell renal cell carcinoma: preliminary findings of The Cancer Genome Atlas–Renal Cell Carcinoma (TCGA–RCC) Imaging Research Group. Abdominal imaging. 2015:1-9.