% Encoding: UTF8

@Book{anatomie,
  title     = {Přehled anatomie člověka},
  publisher = {Univerzita Palackého v Olomouci},
  year      = {2002},
  author    = {Alžběta HOLIBKOVÁ and Stanislav LAICHMAN},
  address   = {Olomouc},
  edition   = {3. vyd.},
  isbn      = {8024404958},
}

@Book{atlas,
  title     = {Kompletní lidské tělo},
  publisher = {Knižní klub},
  year      = {2012},
  author    = {Alice M. ROBERTS},
  address   = {Praha},
  edition   = {Vyd. 1.},
  isbn      = {978-80-242-2958-4},
  subtitle  = {unikátní obrazový průvodce},
}

@Book{anatomie2,
  title     = {Anatomie},
  publisher = {Grada},
  year      = {2011},
  author    = {{\v{C}}IH{\'A}K, R. and GRIM, M. and FEJFAR, O. and Univerzita Karlova. L{\'e}ka{\v{r}}sk{\'a} fakulta, 1. Anatomick{\`y} {\'u}stav},
  isbn      = {9788024738178},
  url       = {https://books.google.cz/books?id=bzZxDwAAQBAJ},
}

@phdthesis{DK,
  title={Indikace dekompresivn{\'\i} kraniektomie u neurotraumat},
  author={JUR{\'A}{\v{N}}, Vil{\'e}m},
  year={2008},
  school={Masarykova univerzita, L{\'e}ka{\v{r}}sk{\'a} fakulta}
}

@phdthesis{CT_rek,
  title={Analysis of iteratively reconstructed CT data: novel methods for measuring image quality},
  author={WALEK, Petr},
  year={2017},
  school={{ Brno University of Technology},  Faculty of Electrical Engineering and Communication, Department of Biomedical Engineering}},
  pages={120}
}

@article{kraniotomie_kraniektomie,
  title={Dekompresivn{\'i} v{\'y}kony u pacient\r{u} s akutn{\v{e}} vzniklou intrakrani{\'a}ln{\'i} hypertenz{\'i}},
  author={MORK, J and MRA{\v{C}}EK, J and {\v{S}}T{\v{E}}P{\'A}NEK, D and P{\v{R}}IB{\'A}{\v{N}}, V},
  journal={84. SVAZEK},
  year={2018},
  pages={89}
}

@Article{kraniotomie,
  author  = {MRÁČEK, J and CHOC, M.},
  title   = {Osteoplastická dekompresivní kraniotomie -indikace a operační technika},
  journal = {Rozhl. Chir.},
  year    = {2010},
  volume  = {89},
  number  = {2},
  pages   = {109-112},
}

@article{hydroxyapatit,
  title={Histological assessment of porous custom-made hydroxyapatite implants 6 months and 2.5 years after cranioplasty},
  author={ONO, HAJIME and SASE, TAIGEN and TANAKA, YUICHIRO and TAKASUNA, HIROSHI},
  journal={Surgical neurology international},
  volume={8},
  year={2017},
  publisher={Wolters Kluwer--Medknow Publications}
}

@article{cranioplasty2017,
  title={Cranioplasty},
  author={PIAZZA, Matthew and GRADY, M Sean},
  journal={Neurosurgery Clinics},
  volume={28},
  number={2},
  pages={257--265},
  year={2017},
  publisher={Elsevier}
}

@article{autologni,
  title={Autologn{\'\i} kranioplastika deponovanou kostn{\'\i} plot{\'e}nkou v podko{\v{z}}{\'\i} mezogastria},
  author={HAMPL, M and HRAB{\'A}LEK, L and VAVERKA, M and KRAHUL{\'I}K, D and NOV{\'A}K, V and HALAJ, M and STEJSKAL, P},
  journal = {Rozhl. Chir.},
  number = {5},
  volume={96},
  year = {2017},
  pages={209--2012},
}

@article{indikace,
  title={Indikace dekompresivn{\'\i} kraniektomie u traumat mozku},
  author={JUR{\'A}{\v{N}}, V and SMR{\v{C}}KA, M and SVOBODA, K and FADRUS, P and {\v{S}}PRL{\'A}KOV{\'A}, A and G{\'A}L, R},
  journal={Cesk Slov Neurol},
  number={5},
  volume={72/105},
  pages={439--445},
  year={2009}
}


@Article{komplikace,
  author  = {D. HRABOVSK{\'Y} and R. JAN{\v{C}}{\'A}LEK and I. {\v{R}}{\'I}HA and J. CHRASTINA},
  title   = {Komplikace kranioplastik po dekompresivn{\'i} kraniektomii},
  journal = {Cesk Slov Neurol N},
  year    = {2016},
  volume={79/112},
  number={1},
  pages   = {77--81},
}

@article{kraniopl_model,
  title={Kranioplastika na modelu},
  author={MASOPUST, V{\'a}clav and H{\"A}CKEL, Martin},
  journal={Vojensk{\'e} zdravotnick{\'e} listy},
  volume={4},
  pages={140--144},
  year={2008}
}

@article{materialy,
  title={Cranioplasty: review of materials and techniques},
  author={AYDIN, SECKIN and KUCUKYURUK, BARIS and ABUZAYED, BASHAR and AYDIN, SABRI and SANUS, GALIP ZIHNI},
  journal={Journal of neurosciences in rural practice},
  volume={2},
  number={2},
  pages={162},
  year={2011},
  publisher={Wolters Kluwer--Medknow Publications}
}

@article{cranioplasty_3Dtisk,
  title={Cranioplasty with a low-cost customized polymethylmethacrylate implant using a desktop 3D printer},
  author={MORALES-G{\'O}MEZ, Jes{\'u}s A and GARCIA-ESTRADA, EVERARDO and LEOS-BORTONI, JORGE E and DELGADO-BRITO, Miriam and FLORES-HUERTA, LUIS E and ADRIANA, A and TORRES-D{\'I}AZ, LUIS J and de LE{\'O}N, {\'A}NGEL R MART{\'I}NEZ-PONCE},
  journal={Journal of neurosurgery},
  volume={130},
  number={5},
  pages={1721--1727},
  year={2018},
  publisher={American Association of Neurological Surgeons}
}
@Article{bioimplants,
author="HO, Chee Meng Benjamin
and Ng, Sum Huan
and Yoon, Yong-Jin",
title="A review on 3D printed bioimplants",
journal="International Journal of Precision Engineering and Manufacturing",
year="2015",
month="May",
day="01",
volume="16",
number="5",
pages="1035--1046",
issn="2005-4602",
doi="10.1007/s12541-015-0134-x",
url="https://doi.org/10.1007/s12541-015-0134-x"
}

@article{PEEK,
  title={The Application of Polyetheretherketone (PEEK) Implants in Cranioplasty},
  author={ZHANG, Jibo and TIAN, Weiqun and CHEN, Jiayi and YU, Jin and ZHANG, Jianjian and CHEN, Jincao},
  journal={Brain research bulletin},
  year={2019},
  publisher={Elsevier}
}

@article{titanium_implant,
  title={Staged reconstruction of large skull defects with soft tissue infection after craniectomy using free flap and cranioplasty with a custom-made titanium mesh constructed by 3D-CT-guided 3D printing technology: Two case reports},
  author={KIM, Seong Hwan and LEE, Seong Joo and LEE, Jun Won and JEONG, Hii Sun and SUH, In Suck},
  journal={Medicine},
  volume={98},
  number={6},
  year={2019},
  publisher={Wolters Kluwer Health}
}

@article{3D_printimplant,
  title={Low-cost customized cranioplasty using a 3D digital printing model: a case report},
  author={DE LA PE{\~N}A, Abel and DE LA PE{\~N}A-BRAMBILA, Javier and P{\'E}REZ-DE LA TORRE, Juan and OCHOA, Miguel and GALLARDO, Guillermo J},
  journal={3D printing in medicine},
  volume={4},
  number={1},
  pages={4},
  year={2018},
  publisher={BioMed Central}
}

@article{kraniotomie_navratil,
  title={Dekompresivn{\'\i} kraniotomie u kraniocerebr{\'a}ln{\'\i}ch poran{\v{e}}n{\'\i}-hodnocen{\'\i} p{\v{r}}e{\v{z}}it{\'\i} a jeho kvality po jednom roce od {\'u}razu},
  author={NAVR{\'A}TIL, Lud{\v{e}}k},
  year={2007},
  journal={Cesk Slov Neurol N},
  volume={70/103},
  number={3},
  pages={294--301},
  publisher={Univerzita Karlova, L{\'e}ka{\v{r}}sk{\'a} fakulta v Plzni}
}

@article{obrazek_edem,
  title={A fatal adverse effect of cefazolin administration: severe brain edema in a patient with multiple meningiomas},
  author={TRIBUDDHARAT, Sirirat and SATHITKARNMANEE, Thepakorn and KITKHUANDEE, Amnat and THEERAPONGPAKDEE, Sunchai and NGAMSAENGSIRISUP, Kriangsak and CHANZHAWONG, Sarinya},
  journal={Drug, healthcare and patient safety},
  volume={8},
  pages={9},
  year={2016},
  publisher={Dove Press}
}

@article{obrazek_extr_edem,
  title={Decompressive craniectomy with massive intractable intraoperative cerebral edema: utilization of silicone sheet for temporary scalp closure: Case report},
  author={AHMADIAN, Amir and BAA J , Ali A and GARCIA, Michael and CAREY, Carolyn and RODRIGUEZ, Luis and STORRS, Bruce and TUITE, Gerald F},
  journal={Journal of Neurosurgery: Pediatrics},
  volume={10},
  number={3},
  pages={195--199},
  year={2012},
  publisher={American Association of Neurological Surgeons}
}


@Misc{obrazek_animace,
  title = {Medical animation: Cranioplasty, {\it High Impact, LLC}},
  url = {https://highimpact.com/exhibits/cranioplasty},
  note = {[Online; navštíveno 20.10.2019]},
  key= {High Impact}
  }
  
@article{obrazek_syndrom1,
author = {JARDINI, A. and LAROSA, Maria and MACEDO, Milton and BERNARDES, L.F. and LAMBERT, C.S. and ZAVAGLIA, Cecília and FILHO, Rubens and CALDERONI, Davi and GHIZONI, Enrico and KHARMANDAYAN, Paulo},
year = {2016},
month = {12},
pages = {203-208},
title = {Improvement in Cranioplasty: Advanced Prosthesis Biomanufacturing},
volume = {49},
journal = {Procedia CIRP},
doi = {10.1016/j.procir.2015.11.017}
}



@article{obrazek_implantat_hydroxyap,
  title={Hydroxyapatite ceramic implants for cranioplasty in children: a single-center experience},
  author={ZACCARIA, Laura and THARAKAN, Sasha Job and ALTERMATT, Stefan},
  journal={Child's nervous system},
  volume={33},
  number={2},
  pages={343--348},
  year={2017},
  publisher={Springer}
}

@Article{softmax,
  author   = {GEIST, MATTHIEU},
  title    = {Soft-max boosting},
  journal  = {Machine Learning},
  year     = {2015},
  volume   = {100},
  number   = {2},
  pages    = {305--332},
  month    = {Sep},
  issn     = {1573-0565},
  day      = {01},
  doi      = {10.1007/s10994-015-5491-2},
  url      = {https://doi.org/10.1007/s10994-015-5491-2},
}

@Book{konvoluce,
  title     = {Digital signal filtering, analysis and restoration},
  publisher = {IET},
  year      = {2000},
  author    = {JAN, Ji{\v{r}}{\'\i}},
  number    = {44},
}





@Article{dropout,
  author  = {SRIVASTAVA, NITISH and HINTON, GEOFFREY E and KRIZHEVSKY, ALEX and SUTSKEVER, ILYA and SALAKHUTDINOV, RUSLAN},
  title   = {Dropout: a simple way to prevent neural networks from overfitting.},
  journal = {{\it Journal of machine learning research}},
  year    = {2014},
  volume  = {15},
  number  = {1},
  pages   = {1929--1958},
}

@Misc{obrazek_titanmesh,
  title = {Patient-specific craniomaxillofacial surgical implants and systems {\it KLS Martin Group}},
  url = {https://3dprint.com/170483/lasercusing-surgical-implants/},
  note = {[Online; navštíveno 21.10.2019]},
  key= {LaserCUSING for 3D Print}
  }


@Misc{obrazek_peek,
  title = {Cranial iD:Patient specific implants {\it Stryker}},
  url = {https://www.stryker.com/us/en/craniomaxillofacial/products/cranial-id.html},
  note = {[Online; navštíveno 21.10.2019]},
  key= {Stryker}
  }

@article{minnema2018ct,
  title={CT image segmentation of bone for medical additive manufacturing using a convolutional neural network},
  author={MINNEMA, Jordi and VAN EIJNATTEN, Maureen and KOUW, Wouter and DIBLEN, Faruk and MENDRIK, Adri{\"e}nne and WOLFF, Jan},
  journal={Computers in biology and medicine},
  volume={103},
  pages={130--139},
  year={2018},
  publisher={Elsevier}
}

@InProceedings{unet,
  author       = {RONNEBERGER, Olaf and FISCHER, Philipp and BROX, Thomas},
  title        = {U-net: Convolutional networks for biomedical image segmentation},
  booktitle    = {International Conference on Medical image computing and computer-assisted intervention},
  year         = {2015},
  pages        = {234--241},
  organization = {Springer},
}

@InCollection{unet++,
  author    = {ZHOU, Zongwei and SIDDIQUEE, Md Mahfuzur Rahman and TAJBAKHSH, Nima and LIANG, Jianming},
  title     = {Unet++: A nested u-net architecture for medical image segmentation},
  booktitle = {Deep Learning in Medical Image Analysis and Multimodal Learning for Clinical Decision Support},
  publisher = {Springer},
  year      = {2018},
  pages     = {3--11},
}

@inproceedings{unet_braintumor,
  title={Automatic brain tumor detection and segmentation using U-Net based fully convolutional networks},
  author={DONG, Hao and YANG, Guang and LIU, Fangde and MO, Yuanhan and GUO, Yike},
  booktitle={annual conference on medical image understanding and analysis},
  pages={506--517},
  year={2017},
  organization={Springer}
}

@InProceedings{3d_unet_sparse,
  author       = {{\c{C}}I{\c{C}}EK, {\"O}zg{\"u}n and ABDULKADIR, Ahmed and LIENKAMP, Soeren S and BROX, Thomas and RONNEBERGER, Olaf},
  title        = {3D U-Net: learning dense volumetric segmentation from sparse annotation},
  booktitle    = {International conference on medical image computing and computer-assisted intervention},
  year         = {2016},
  pages        = {424--432},
  organization = {Springer},
}


@article{unet_recurrent,
  title={Recurrent residual convolutional neural network based on u-net (R2U-net) for medical image segmentation},
  author={ALOM, Md Zahangir and HASAN, Mahmudul and YAKOPCIC, Chris and TAHA, Tarek M and ASARI, Vijayan K},
  journal={arXiv preprint arXiv:1802.06955},
  year={2018}
}


@InProceedings{3Dunet,
  author       = {CHEN, Xuhui and LU, Yi and BAI, Junjie and YIN, Youbing and CAO, Kunlin and LI, Yuwei and CHEN, Hanbo and SONG, Qi and WU, Jun},
  title        = {Train a 3D U-Net to segment cranial vasculature in CTA volume without manual annotation},
  booktitle    = {2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018)},
  year         = {2018},
  pages        = {559--563},
  organization = {IEEE},
}


@Book{drastich,
  title     = {Tomografick{\'e} zobrazovac{\'\i} syst{\'e}my},
  publisher = {Vysok{\'e} u{\v{c}}en{\'\i} technick{\'e} v Brn{\v{e}}, Fakulta elektrotechniky a informatiky},
  year      = {2004},
  author    = {DRASTICH, Ale{\v{s}}}
}

@Book{bushberg,
  title     = {The Essential Physics of Medical Imaging},
  publisher = {Wolters Kluwer Health},
  year      = {2011},
  author    = {BUSHBERG, J.T. and SEIBERT, J.A. and LEIDHOLDT, E.M. and BOONE, J.M.},
  isbn      = {9781451153941},
  url       = {https://books.google.cz/books?id=RKcTgTqeniwC},
}

@article{iter_rek,
  title={Iterative reconstruction methods in X-ray CT},
  author={BEISTER, Marcel and KOLDITZ, Daniel and KALENDER, Willi A},
  journal={Physica medica},
  volume={28},
  number={2},
  pages={94--108},
  year={2012},
  publisher={Elsevier}
}

@book{JJ_book,
  title={Medical image processing, reconstruction and restoration: concepts and methods},
  author={JAN, Jiri},
  year={2005},
  publisher={CRC Press}
}

@article{spanel_segmentace,
  title={Obrazov{\'e} segmenta{\v{c}}n{\'\i} techniky: P{\v{r}}ehled existuj{\'\i}c{\'\i}ch metod [online]},
  author={{\v{S}}PAN{\v{E}}L, Michal and BERAN, V{\'\i}t{\v{e}}zslav},
  url = {http://www.fit.vutbr.cz/~spanel/segmentace/},
  year={2006}
}

@book{kniha_deeplearningwithpython,
  title={Deep Learning with Python},
  author={CHOLLET, Francois},
 isbn = {1617294438, 9781617294433},
  year={2018},
  edition = {1st},
 publisher = {Manning Publications Co.}
}

@book{bishop_kniha,
  title={Pattern recognition and machine learning},
  author={BISHOP, Christopher M},
  year={2006},
  publisher={Springer Science+ Business Media},
  isbn ={0387310738}
}

@Misc{cnn,
  author = {KARPATHY, A.},
  title  = {{\it Convolutional Neural Networks for Visual Recognition}},
  note   = {[Online; navštíveno 21.9.2019]},
  url    = {http://cs231n.github.io/},
}


@article{iter_rek2,
  title={Iterative reconstruction techniques for computed tomography Part 1: technical principles},
  author={WILLEMINK, Martin J and DE JONG, Pim A and LEINER, Tim and DE HEER, Linda M and NIEVELSTEIN, Rutger AJ and BUDDE, Ricardo PJ and SCHILHAM, Arnold MR},
  journal={European radiology},
  volume={23},
  number={6},
  pages={1623--1631},
  year={2013},
  publisher={Springer}
}

@Misc{tutorial,
  author = {TensorFlow},
  title  = {Image segmentation},
  url    = {https://www.tensorflow.org/tutorials/images/segmentation},
}

@Misc{umela_intelegence,
  author       = {KOZUMPLÍK, J. and PROVAZNÍK, I.},
  title        = {{\it Umělá inteligence v medicíně}: elektronická skripta},
  howpublished = {ÚBMI FEKT VUT v Brně},
  year         = {2007},
  note         = {\textsc{B}rno},
}

@inproceedings{focal,
  title={Focal loss for dense object detection},
  author={LIN, Tsung-Yi and GOYAL, Priya and GIRSHICK, Ross and HE, Kaiming and DOLL{\'A}A, Piotr},
  booktitle={Proceedings of the IEEE international conference on computer vision},
  pages={2980--2988},
  year={2017}
}

@incollection{dice_loss,
  title={Generalised dice overlap as a deep learning loss function for highly unbalanced segmentations},
  author={SUDRE, Carole H and LI, Wenqi and VERCAUTEREN, Tom and OURSELIN, Sebastien and CARDOSO, M Jorge},
  booktitle={Deep learning in medical image analysis and multimodal learning for clinical decision support},
  pages={240--248},
  year={2017},
  publisher={Springer}
}

@inproceedings{mobilenetv2,
  title={Mobilenetv2: Inverted residuals and linear bottlenecks},
  author={SANDLER, Mark and HOWARD, Andrew and ZHU, Menglong and ZHMOGINOV, Andrey and CHEN, Liang-Chieh},
  booktitle={Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition},
  pages={4510--4520},
  year={2018}
}

@article{jaccard_ind,
  title={The probabilistic basis of Jaccard's index of similarity},
  author={REAL, Raimundo and VARGAS, Juan M},
  journal={Systematic biology},
  volume={45},
  number={3},
  pages={380--385},
  year={1996},
  publisher={Society of Systematic Biologists}
}

@inproceedings{seman_seg,
  title={Fully convolutional networks for semantic segmentation},
  author={LONG, Jonathan and SHELHAMER, Evan and DARRELL, Trevor},
  booktitle={Proceedings of the IEEE conference on computer vision and pattern recognition},
  pages={3431--3440},
  year={2015}
}

@inproceedings{unet3D,
  title={3D U-Net: learning dense volumetric segmentation from sparse annotation},
  author={{\c{C}}I{\c{C}}EK, {\"O}zg{\"u}n and ABDULKADIR, Ahmed and LIENKAMP, Soeren S and BROX, Thomas and RONNEBERGER, Olaf},
  booktitle={International conference on medical image computing and computer-assisted intervention},
  pages={424--432},
  year={2016},
  organization={Springer}
}

@misc{3d_unet_rep,
  author = {ELIS, David G},
  title = {3DUnetCNN},
  year = {2018},
  publisher = {GitHub},
  journal = {GitHub repository},
  howpublished = {\url{https://github.com/ellisdg/3DUnetCNN}},
  organization={University of Nebraska Medical Center}
}

@book{normalizace,
  title={Molecular Imaging I},
  author={HOFMANN, F and SCHWAIGER, Markus and SEMMLER, Wolfhard},
  year={2008},
  publisher={Springer-Verlag Berlin Heidelberg}
}


@incollection{GD_a_SGD,
  title={Large-scale machine learning with stochastic gradient descent},
  author={BOTTOU, L{\'e}on},
  booktitle={Proceedings of COMPSTAT'2010},
  pages={177--186},
  year={2010},
  publisher={Springer}
}

@book{deep_learning_goodfellow,
  title={Deep learning},
  author={GOODFELLOW, Ian and BENGIO, Yoshua and COURVILLE, Aaron},
  year={2016},
  publisher={MIT press}
}