TY - JOUR AU - Irobalieva, R. N. AU - Martins, B. AU - Medalia, O. PY - 2016 DA - 2016// TI - Cellular structural biology as revealed by cryo-electron tomography JO - J Cell Sci VL - 129 UR - https://doi.org/10.1242/jcs.171967 DO - 10.1242/jcs.171967 ID - Irobalieva2016 ER - TY - JOUR AU - Woodward, C. L. AU - Mendonċa, L. M. AU - Jensen, G. J. PY - 2015 DA - 2015// TI - Direct visualization of vaults within intact cells by electron cryo-tomography JO - Cell Mol Life Sci VL - 72 UR - https://doi.org/10.1007/s00018-015-1898-y DO - 10.1007/s00018-015-1898-y ID - Woodward2015 ER - TY - JOUR AU - Elad, N. AU - Volberg, T. AU - Patla, I. AU - Hirschfeld-Warneken, V. AU - Grashoff, C. AU - Spatz, J. P. PY - 2013 DA - 2013// TI - The role of integrin-linked kinase in the molecular architecture of focal adhesions JO - J Cell Sci VL - 126 UR - https://doi.org/10.1242/jcs.120295 DO - 10.1242/jcs.120295 ID - Elad2013 ER - TY - JOUR AU - Grossman, E. AU - Medalia, O. AU - Zwerger, M. PY - 2012 DA - 2012// TI - Functional Architecture of the Nuclear Pore Complex JO - Annu Rev Biophys VL - 41 UR - https://doi.org/10.1146/annurev-biophys-050511-102328 DO - 10.1146/annurev-biophys-050511-102328 ID - Grossman2012 ER - TY - BOOK AU - Berdanier, C. D. PY - 2005 DA - 2005// TI - Mitochondria in health and disease. PB - CRC Press CY - Boca Raton UR - https://doi.org/10.1201/9781420028843 DO - 10.1201/9781420028843 ID - Berdanier2005 ER - TY - JOUR AU - Asano, S. AU - Engel, B. D. AU - Baumeister, W. PY - 2016 DA - 2016// TI - In Situ Cryo-Electron Tomography: A Post-Reductionist Approach to Structural Biology JO - J Mol Biol VL - 428 UR - https://doi.org/10.1016/j.jmb.2015.09.030 DO - 10.1016/j.jmb.2015.09.030 ID - Asano2016 ER - TY - JOUR AU - Volkmann, N. PY - 2002 DA - 2002// TI - A novel three-dimensional variant of the watershed transform for segmentation of electron density maps JO - J Struct Biol VL - 138 UR - https://doi.org/10.1016/S1047-8477(02)00009-6 DO - 10.1016/S1047-8477(02)00009-6 ID - Volkmann2002 ER - TY - JOUR AU - Cyrklaff, M. AU - Risco, C. AU - Fernández, J. J. AU - Jiménez, M. V. AU - Estéban, M. AU - Baumeister, W. PY - 2005 DA - 2005// TI - Cryo-electron tomography of vaccinia virus JO - Proc Natl Acad Sci VL - 102 UR - https://doi.org/10.1073/pnas.0409825102 DO - 10.1073/pnas.0409825102 ID - Cyrklaff2005 ER - TY - JOUR AU - Martinez-Sanchez, A. AU - Garcia, I. AU - Fernandez, J. J. PY - 2011 DA - 2011// TI - A differential structure approach to membrane segmentation in electron tomography JO - J Struct Biol VL - 175 UR - https://doi.org/10.1016/j.jsb.2011.05.010 DO - 10.1016/j.jsb.2011.05.010 ID - Martinez-Sanchez2011 ER - TY - JOUR AU - Sandberg, K. AU - Brega, M. PY - 2007 DA - 2007// TI - Segmentation of thin structures in electron micrographs using orientation fields JO - J Struct Biol VL - 157 UR - https://doi.org/10.1016/j.jsb.2006.09.007 DO - 10.1016/j.jsb.2006.09.007 ID - Sandberg2007 ER - TY - CHAP AU - Loss, L. A. AU - Bebis, G. AU - Chang, H. AU - Auer, M. AU - Sarkar, P. AU - Parvin, B. PY - 2012 DA - 2012// TI - Automatic Segmentation and Quantification of Filamentous Structures in Electron Tomography BT - Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine. BCB ’12 PB - ACM CY - New York ID - Loss2012 ER - TY - JOUR AU - Xu, M. AU - Alber, F. PY - 2013 DA - 2013// TI - Automated target segmentation and real space fast alignment methods for high-throughput classification and averaging of crowded cryo-electron subtomograms JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/btt225 DO - 10.1093/bioinformatics/btt225 ID - Xu2013 ER - TY - JOUR AU - Zeng, X. AU - Leung, M. R. AU - Zeev-Ben-Mordehai, T. AU - Xu, M. PY - 2018 DA - 2018// TI - A convolutional autoencoder approach for mining features in cellular electron cryo-tomograms and weakly supervised coarse segmentation JO - J Struct Biol VL - 202 UR - https://doi.org/10.1016/j.jsb.2017.12.015 DO - 10.1016/j.jsb.2017.12.015 ID - Zeng2018 ER - TY - JOUR AU - Luengo, I. AU - Darrow, M. C. AU - Spink, M. C. AU - Sun, Y. AU - Dai, W. AU - He, C. Y. PY - 2017 DA - 2017// TI - SuRVoS: Super-Region Volume Segmentation workbench JO - J Struct Biol VL - 198 UR - https://doi.org/10.1016/j.jsb.2017.02.007 DO - 10.1016/j.jsb.2017.02.007 ID - Luengo2017 ER - TY - JOUR AU - Chen, M. AU - Dai, W. AU - Sun, S. Y. PY - 2017 DA - 2017// TI - Convolutional neural Networks for automated annotation of cellular cryo-electron tomograms JO - Nat Methods VL - 14 UR - https://doi.org/10.1038/nmeth.4405 DO - 10.1038/nmeth.4405 ID - Chen2017 ER - TY - CHAP AU - Girshick, R. AU - Donahue, J. AU - Darrell, T. AU - Malik, J. PY - 2013 DA - 2013// TI - Rich feature hierarchies for accurate object detection and semantic segmentation BT - 2014 IEEE Conference on Computer Vision and Pattern Recognition PB - IEEE CY - Columbus ID - Girshick2013 ER - TY - CHAP AU - Ren, S. AU - He, K. AU - Girshick, R. AU - Sun, J. ED - Cortes, C. ED - Lawrence, N. D. ED - Lee, D. D. ED - Sugiyama, M. ED - Garnett, R. PY - 2015 DA - 2015// TI - Faster R-CNN: Towards Real-Time Object Detection with Region Proposal Networks BT - Advances in Neural Information Processing Systems 28 PB - Curran Associates, Inc. CY - Red Hook ID - Ren2015 ER - TY - JOUR AU - Xu, M. AU - Papageorgiou, D. P. AU - Abidi, S. Z. AU - Dao, M. AU - Zhao, H. AU - Karniadakis, G. E. PY - 2017 DA - 2017// TI - A deep convolutional neural network for classification of red blood cells in sickle cell anemia JO - PLoS Comput Biol VL - 13 UR - https://doi.org/10.1371/journal.pcbi.1005746 DO - 10.1371/journal.pcbi.1005746 ID - Xu2017 ER - TY - STD TI - Wang W, Taft DA, Chen YJ, Zhang J, Wallace CT, Xu M, et al.Learn to segment single cells with deep distance estimator and deep cell detector. arXiv preprint arXiv:180310829. 2018. ID - ref19 ER - TY - CHAP AU - Tomasi, C. AU - Manduchi, R. PY - 1998 DA - 1998// TI - Bilateral filtering for gray and color images BT - Sixth International Conference on Computer Vision (IEEE Cat. No.98CH36271). PB - IEEE CY - Bombay ID - Tomasi1998 ER - TY - CHAP AU - He, K. AU - Zhang, X. AU - Ren, S. AU - Sun, J. PY - 2016 DA - 2016// TI - Deep Residual Learning for Image Recognition BT - The IEEE Conference on Computer Vision and Pattern Recognition (CVPR) PB - IEEE CY - Las Vegas ID - He2016 ER - TY - STD TI - Keras-frcnn HY. GitHub. 2017. https://github.com/yhenon/keras-frcnn. Accessed 25 July 2018. UR - https://github.com/yhenon/keras-frcnn ID - ref22 ER - TY - CHAP AU - Deng, J. AU - Dong, W. AU - Socher, R. AU - Li, L. J. AU - Li, K. AU - Fei-Fei, L. PY - 2009 DA - 2009// TI - ImageNet: A Large-Scale Hierarchical Image Database BT - CVPR09. PB - IEEE CY - Miami ID - Deng2009 ER - TY - STD TI - Tzutalin. LabelImg. GitHub. 2015. https://github.com/tzutalin/labelImg. Accessed 05 Apr 2018. UR - https://github.com/tzutalin/labelImg ID - ref24 ER - TY - STD TI - Thong JT, Sim KS, Phang JC. Single-image signal-to-noise ratio estimation. Scanning; 23(5):328–336. ID - ref25 ER - TY - STD TI - Chollet F, et al.Keras. GitHub. 2015. https://github.com/fchollet/keras. Accessed 25 July 2018. UR - https://github.com/fchollet/keras ID - ref26 ER - TY - CHAP AU - Abadi, M. AU - Barham, P. AU - Chen, J. AU - Chen, Z. AU - Davis, A. AU - Dean, J. PY - 2016 DA - 2016// TI - TensorFlow: A system for large-scale machine learning BT - 12th USENIX Symposium on Operating Systems Design and Implementation (OSDI 16) PB - USENIX Association CY - Berkeley ID - Abadi2016 ER - TY - STD TI - Kingma DP, Ba J. Adam: A Method for Stochastic Optimization. arXiv preprint arXiv:14126980. 2014. ID - ref28 ER -