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Ha J, Alvino C, Pryor G, Niethammer M, Johnson E, Tannenbaum A.  2004.  Active Contours and Optical Flow for Automatic Tracking of Flying Vehicles. Proceedings of the American Control Conference. 4:3441–3446.
Niethammer M, Pohl K  M, Janoos F, Wells, III W  M.  2017.  Active Mean Fields for Probabilistic Image Segmentation: Connections with Chan-Vese and Rudin-Osher-Fatemi Models. ArXiv e-prints; accepted to SIAM Journal on Imaging Science. PDF icon Active Mean Fields for Probabilistic Image Segmentation (10.02 MB)
Dixit M, Kwitt R, Niethammer M, Vasconcelos N.  2017.  AGA: Attribute Guided Augmentation. CVPR. PDF icon aga2017.pdf (483.13 KB)
Niethammer M, Stein AN, Kalies WD, Pilarczyk P, Mischaikow K, Tannenbaum A.  2002.  Analysis of blood vessel topology by cubical homology. Proceedings of the International Conference on Image Processing. 2:969–972.PDF icon niethammer2002_ICIP_cubical_homology.pdf (93.82 KB)
Niethammer M, Borland D, Marron JS, Woolsey J, Thomas NE.  2010.  Appearance Normalization of Histology Slides. MICCAI, International Workshop Machine Learning in Medical Imaging. PDF icon niethammer2010_color_correction.pdf (1.56 MB)
Vicory J, Couture HD, Thomas NE, Borland D, Marron JS, Woosley J, Niethammer M.  2015.  Appearance Normalization of Histology Slides. Computerized Medical Imaging and Graphics. PDF icon vicory2015_appearancenorm.pdf (13.47 MB)
Niethammer M, Betelu S, Sapiro G, Tannenbaum A, Giblin PJ.  2004.  Area-based medial axis of planar curves. International Journal of Computer Vision. 60:203–224.PDF icon niethammer2004_IJCV_area_based_medial_axis_of_planar_curves.pdf (892.39 KB)
Kerber F, Sprenger H, Niethammer M, Luangvilai K, Jacobs L.  2010.  Attenuation analysis of Lamb waves using the chirplet transform. EURASIP: Journal on Advances in Signal Processing.
Hurlebaus S, Niethammer M, Jacobs LJ, Valle C.  2001.  Automated methodology to locate notches with Lamb waves. Acoustic Research Letters Online. 2:97–102.PDF icon hurlebaus2001_ARLO_automated_methodology_to_locate_notches_with_lamb_waves.pdf (1.52 MB)
Li W, Ibanez L, Gelas A, Yeo BTT, Niethammer M, Andreasen NC, Magnotta VA.  2011.  An automated pipeline for cortical surface generation and registration of the cerebral cortex. Proceedings of SPIE. 7962:796229.
Shan L, Zach C, Charles C, Niethammer M.  2014.  Automatic Atlas-based Three-label Cartilage Segmentation from MR Knee Images. Medical Image Analysis. PDF icon shan2014_media_cartilage_segmentation.pdf (5.2 MB)
Shan L, Charles C, Niethammer M.  2011.  Automatic Atlas-based Three-label Cartilage Segmentation from MR Knee Images. Proceedings of the Workshop on Mathematical Methods in Biomedical Image Analysis (MMBIA). PDF icon shan_MMBIA2012.pdf (2.57 MB)
Shan L, Zach C, Styner M, Charles C, Niethammer M.  2010.  Automatic Bone Segmentation and Alignment from MR knee images. SPIE Medical Imaging. PDF icon shan2010_SPIE.pdf (1.25 MB)
Lee J, Ehlers C, Crews F, Niethammer M, Budin F, Paniagua B, Sulik K, Johns J, Styner M, Oguz I.  2011.  Automatic cortical thickness analysis on rodent brain. Proceedings of SPIE. 7962:796248.
Shan L.  2014.  Automatic localized analysis of longitudinal cartilage changes.
Shan L, Charles C, Niethammer M.  2012.  Automatic Multi-Atlas-Based Cartilage Segmentation from Knee MR Images. Proceedings of the International Symposium on Biomedical Imaging (ISBI). PDF icon shan_isbi_2012.pdf (3.64 MB)
Shan L, Zach C, Niethammer M.  2010.  Automatic three-label bone segmentation from knee MR images. International Symposium on Biomedical Imaging (ISBI). PDF icon shan2010_isbi.pdf (1.16 MB)
Kaplan E, Min J-Y, Ke Q, Chen Y, Niethammer M, Rana JS, Malek S, Verheugt FWA, Morgan JP.  2009.  Calcium and cyclic nucleotides affect TNF-alpha-induced stem cell migration.. Biochemical and biophysical research communications. 382(2):241-6.
Vela PA, Niethammer M, Malcolm J, Tannenbaum A.  2005.  Closed Loop Visual Tracking Using Observer-Based Dynamic Active Contours. Proceedings of the Conference on Guidance Navigation and Control. PDF icon vela_acc.pdf (162.6 KB)
Pichon E, Niethammer M, Sapiro G.  2003.  Color histogram equalization through mesh deformation. Proceedings of the International Conference on Image Processing. :117–120.PDF icon pichon2003_ICIP_color_histogram_equalization_through_mesh_deformation.pdf (1.27 MB)
Stanely N., Kwitt R, Niethammer M., Mucha P..  2017.  Compressing Networks with Super Nodes. arXiv.
Hofer C., Kwitt R, Niethammer M., Hoeller Y., Trinka E., Uhl A..  2017.  Constructing Shape Spaces from a Topological Perspective. Proceedings of the International Conference on Information Processing in Medical Imaging (IPMI). PDF icon hofer2017_ipmi.pdf (492.78 KB)
Zach C, Niethammer M, Frahm J-M.  2009.  Continuous Maximal Flows and Wulff Shapes: Application to MRFs. Proceedings of the Conference on Computer Vision and Pattern Recognition (CVPR). :1911–1918.PDF icon zach_cvpr2009a-preprint.pdf (1.46 MB)
Oguz I, Niethammer M, Cates J, Whitaker R, Fletcher T, Styner M.  2009.  Cortical Correspondence with Probabilistic Fiber Connectivity. Proceedings of the Conference on Information Processing in Medical Imaging (IPMI). :651–663.PDF icon oguz2009_ipmi.pdf (4.89 MB)