My publications

Journals

Interactive segmentation in MRI for orthopedic surgery planning: bone tissue

Ozdemir, Firat and Karani, Neerav and Fürnstahl, Philipp and Goksel, Orcun. 2017. International journal of computer assisted radiology and surgery. 12, 1031--1039.

Registration of 3D freehand ultrasound to a bone model for orthopedic procedures of the forearm

Ciganovic, Matija and Ozdemir, Firat and Pean, Fabien and Fuernstahl, Philipp and Tanner, Christine and Goksel, Orcun. 2018. International journal of computer assisted radiology and surgery. 13, 827--836.

Extending pretrained segmentation networks with additional anatomical structures

Ozdemir, Firat and Goksel, Orcun. 2019. International journal of computer assisted radiology and surgery. 14, 1187--1195.

Active learning for segmentation based on Bayesian sample queries

Ozdemir, Firat and Peng, Zixuan and Fuernstahl, Philipp and Tanner, Christine and Goksel, Orcun. 2021. Knowledge-Based Systems. 214, 106531.

A Bayesian data assimilation framework for lake 3D hydrodynamic models with a physics-preserving particle filtering method using SPUX-MITgcm v1

Safin, Artur and Casañas, Ramón and Luz, Cintia and Cubero Cardoso, Juan and Serrano Moral, Antonio and Gorrasi, Susanna and Muñoz Palazón, Barbara and Aranda Ballesteros, Elisabet. 2021. Geosci Model Dev Discuss. 2021, 1--22.

Learning summary statistics for bayesian inference with autoencoders

Albert, Carlo and Ulzega, Simone and Ozdemir, Firat and Perez-Cruz, Fernando and Mira, Antonietta. 2022. SciPost Physics Core. 5, 043.

A Bayesian data assimilation framework for lake 3D hydrodynamic models with a physics-preserving particle filtering method using SPUX-MITgcm v1

Safin, Artur and Bouffard, Damien and Ozdemir, Firat and Ramón, Cintia L and Runnalls, James and Georgatos, Fotis and Minaudo, Camille and Šukys, Jonas. 2022. Geoscientific Model Development. 15, 7715--7730.

Conference proceedings

A decision forest based feature selection framework for action recognition from rgb-depth cameras

Negin, Farhood and Ozdemir, Firat and Akgül, Ceyhun Burak and Yüksel, Kamer Ali and Ercil, Aytül. 2013. Image Analysis and Recognition: 10th International Conference, ICIAR 2013, Povoa do Varzim, Portugal, June 26-28, 2013. Proceedings 10. 648--657. Springer Berlin Heidelberg.

Graphical modeling of ultrasound propagation in tissue for automatic bone segmentation

Ozdemir, Firat and Ozkan, Ece and Goksel, Orcun. 2016. Medical Image Computing and Computer-Assisted Intervention--MICCAI 2016: 19th International Conference, Athens, Greece, October 17-21, 2016, Proceedings, Part II 19. 256--264. Springer International Publishing.

Automatic segmentation of abdominal MRI using selective sampling and random walker

Thoma, Janine and Ozdemir, Firat and Goksel, Orcun. 2017. Medical Computer Vision and Bayesian and Graphical Models for Biomedical Imaging: MICCAI 2016 International Workshops, MCV and BAMBI, Athens, Greece, October 21, 2016, Revised Selected Papers 8. 83--93. Springer International Publishing.

Learn the new, keep the old: Extending pretrained models with new anatomy and images

Ozdemir, Firat and Fuernstahl, Philipp and Goksel, Orcun. 2018. Medical Image Computing and Computer Assisted Intervention--MICCAI 2018: 21st International Conference, Granada, Spain, September 16-20, 2018, Proceedings, Part IV 11. 361--369. Springer International Publishing.

Active learning for segmentation by optimizing content information for maximal entropy

Ozdemir, Firat and Peng, Zixuan and Tanner, Christine and Fuernstahl, Philipp and Goksel, Orcun. 2018. Deep Learning in Medical Image Analysis and Multimodal Learning for Clinical Decision Support: 4th International Workshop, DLMIA 2018, and 8th International Workshop, ML-CDS 2018, Held in Conjunction with MICCAI 2018, Granada, Spain, September 20, 2018, Proceedings 4. 183--191. Springer International Publishing.

Deep learning techniques for bone surface delineation in ultrasound

Ciganovic, Matija and Ozdemir, Firat and Farshad, Mazda and Göksel, Orcun. 2019. Medical Imaging 2019: Ultrasonic Imaging and Tomography. 224--230. SPIE.

Signal Domain Learning Approach for Optoacoustic Image Reconstruction from Limited View Data

Susmelj, Anna Klimovskaia and Lafci, Berkan and Ozdemir, Firat and Davoudi, Neda and Dean-Ben, Xose Luis and Perez-Cruz, Fernando and Razansky, Daniel. 2022. International Conference on Medical Imaging with Deep Learning. 1173--1191. PMLR.

Retrospective Uncertainties for Deep Models using Vine Copulas

Tagasovska, Nataša and Ozdemir, Firat and Brando, Axel. 2023. International Conference on Artificial Intelligence and Statistics (AISTATS). . .

Scientific reports

Generative adversarial networks for MR-CT deformable image registration

Tanner, Christine and Ozdemir, Firat and Profanter, Romy and Vishnevsky, Valeriy and Konukoglu, Ender and Goksel, Orcun. 2018. arXiv preprint arXiv:1807.07349

Delineating Bone Surfaces in B-Mode Images Constrained by Physics of Ultrasound Propagation

Ozdemir, Firat and Tanner, Christine and Goksel, Orcun. 2020. arXiv preprint arXiv:2001.02001

Probabilistic modeling of lake surface water temperature using a Bayesian spatio-temporal graph convolutional neural network

Stalder, Michael and Ozdemir, Firat and Safin, Artur and Sukys, Jonas and Bouffard, Damien and Perez-Cruz, Fernando. 2021. arXiv preprint arXiv:2109.13235

Building a physics-constrained, fast and stable machine learning-based radiation emulator

Bertoli, Guillaume and Schemm, Sebastian and Ozdemir, Firat and Szekely, Eniko and Cruz, Fernando Perez. 2022. Copernicus Meetings