Search Results for author: Sandy Engelhardt

Found 25 papers, 15 papers with code

Investigating Data Memorization in 3D Latent Diffusion Models for Medical Image Synthesis

no code implementations3 Jul 2023 Salman Ul Hassan Dar, Arman Ghanaat, Jannik Kahmann, Isabelle Ayx, Theano Papavassiliu, Stefan O. Schoenberg, Sandy Engelhardt

Despite the promise, the capacity of such models to memorize sensitive patient training data and synthesize samples showing high resemblance to training data samples is relatively unexplored.

Contrastive Learning Image Generation +1

Surgical Phase and Instrument Recognition: How to identify appropriate Dataset Splits

1 code implementation29 Jun 2023 Georgii Kostiuchik, Lalith Sharan, Benedikt Mayer, Ivo Wolf, Bernhard Preim, Sandy Engelhardt

It focuses on the visualization of the occurrence of phases, phase transitions, instruments, and instrument combinations across sets.

Data Visualization Instrument Recognition

Why is the winner the best?

no code implementations CVPR 2023 Matthias Eisenmann, Annika Reinke, Vivienn Weru, Minu Dietlinde Tizabi, Fabian Isensee, Tim J. Adler, Sharib Ali, Vincent Andrearczyk, Marc Aubreville, Ujjwal Baid, Spyridon Bakas, Niranjan Balu, Sophia Bano, Jorge Bernal, Sebastian Bodenstedt, Alessandro Casella, Veronika Cheplygina, Marie Daum, Marleen de Bruijne, Adrien Depeursinge, Reuben Dorent, Jan Egger, David G. Ellis, Sandy Engelhardt, Melanie Ganz, Noha Ghatwary, Gabriel Girard, Patrick Godau, Anubha Gupta, Lasse Hansen, Kanako Harada, Mattias Heinrich, Nicholas Heller, Alessa Hering, Arnaud Huaulmé, Pierre Jannin, Ali Emre Kavur, Oldřich Kodym, Michal Kozubek, Jianning Li, Hongwei Li, Jun Ma, Carlos Martín-Isla, Bjoern Menze, Alison Noble, Valentin Oreiller, Nicolas Padoy, Sarthak Pati, Kelly Payette, Tim Rädsch, Jonathan Rafael-Patiño, Vivek Singh Bawa, Stefanie Speidel, Carole H. Sudre, Kimberlin Van Wijnen, Martin Wagner, Donglai Wei, Amine Yamlahi, Moi Hoon Yap, Chun Yuan, Maximilian Zenk, Aneeq Zia, David Zimmerer, Dogu Baran Aydogan, Binod Bhattarai, Louise Bloch, Raphael Brüngel, Jihoon Cho, Chanyeol Choi, Qi Dou, Ivan Ezhov, Christoph M. Friedrich, Clifton Fuller, Rebati Raman Gaire, Adrian Galdran, Álvaro García Faura, Maria Grammatikopoulou, SeulGi Hong, Mostafa Jahanifar, Ikbeom Jang, Abdolrahim Kadkhodamohammadi, Inha Kang, Florian Kofler, Satoshi Kondo, Hugo Kuijf, Mingxing Li, Minh Huan Luu, Tomaž Martinčič, Pedro Morais, Mohamed A. Naser, Bruno Oliveira, David Owen, Subeen Pang, Jinah Park, Sung-Hong Park, Szymon Płotka, Elodie Puybareau, Nasir Rajpoot, Kanghyun Ryu, Numan Saeed, Adam Shephard, Pengcheng Shi, Dejan Štepec, Ronast Subedi, Guillaume Tochon, Helena R. Torres, Helene Urien, João L. Vilaça, Kareem Abdul Wahid, Haojie Wang, Jiacheng Wang, Liansheng Wang, Xiyue Wang, Benedikt Wiestler, Marek Wodzinski, Fangfang Xia, Juanying Xie, Zhiwei Xiong, Sen yang, Yanwu Yang, Zixuan Zhao, Klaus Maier-Hein, Paul F. Jäger, Annette Kopp-Schneider, Lena Maier-Hein

The "typical" lead of a winning team is a computer scientist with a doctoral degree, five years of experience in biomedical image analysis, and four years of experience in deep learning.

Benchmarking Multi-Task Learning

Biomedical image analysis competitions: The state of current participation practice

no code implementations16 Dec 2022 Matthias Eisenmann, Annika Reinke, Vivienn Weru, Minu Dietlinde Tizabi, Fabian Isensee, Tim J. Adler, Patrick Godau, Veronika Cheplygina, Michal Kozubek, Sharib Ali, Anubha Gupta, Jan Kybic, Alison Noble, Carlos Ortiz de Solórzano, Samiksha Pachade, Caroline Petitjean, Daniel Sage, Donglai Wei, Elizabeth Wilden, Deepak Alapatt, Vincent Andrearczyk, Ujjwal Baid, Spyridon Bakas, Niranjan Balu, Sophia Bano, Vivek Singh Bawa, Jorge Bernal, Sebastian Bodenstedt, Alessandro Casella, Jinwook Choi, Olivier Commowick, Marie Daum, Adrien Depeursinge, Reuben Dorent, Jan Egger, Hannah Eichhorn, Sandy Engelhardt, Melanie Ganz, Gabriel Girard, Lasse Hansen, Mattias Heinrich, Nicholas Heller, Alessa Hering, Arnaud Huaulmé, Hyunjeong Kim, Bennett Landman, Hongwei Bran Li, Jianning Li, Jun Ma, Anne Martel, Carlos Martín-Isla, Bjoern Menze, Chinedu Innocent Nwoye, Valentin Oreiller, Nicolas Padoy, Sarthak Pati, Kelly Payette, Carole Sudre, Kimberlin Van Wijnen, Armine Vardazaryan, Tom Vercauteren, Martin Wagner, Chuanbo Wang, Moi Hoon Yap, Zeyun Yu, Chun Yuan, Maximilian Zenk, Aneeq Zia, David Zimmerer, Rina Bao, Chanyeol Choi, Andrew Cohen, Oleh Dzyubachyk, Adrian Galdran, Tianyuan Gan, Tianqi Guo, Pradyumna Gupta, Mahmood Haithami, Edward Ho, Ikbeom Jang, Zhili Li, Zhengbo Luo, Filip Lux, Sokratis Makrogiannis, Dominik Müller, Young-tack Oh, Subeen Pang, Constantin Pape, Gorkem Polat, Charlotte Rosalie Reed, Kanghyun Ryu, Tim Scherr, Vajira Thambawita, Haoyu Wang, Xinliang Wang, Kele Xu, Hung Yeh, Doyeob Yeo, Yixuan Yuan, Yan Zeng, Xin Zhao, Julian Abbing, Jannes Adam, Nagesh Adluru, Niklas Agethen, Salman Ahmed, Yasmina Al Khalil, Mireia Alenyà, Esa Alhoniemi, Chengyang An, Talha Anwar, Tewodros Weldebirhan Arega, Netanell Avisdris, Dogu Baran Aydogan, Yingbin Bai, Maria Baldeon Calisto, Berke Doga Basaran, Marcel Beetz, Cheng Bian, Hao Bian, Kevin Blansit, Louise Bloch, Robert Bohnsack, Sara Bosticardo, Jack Breen, Mikael Brudfors, Raphael Brüngel, Mariano Cabezas, Alberto Cacciola, Zhiwei Chen, Yucong Chen, Daniel Tianming Chen, Minjeong Cho, Min-Kook Choi, Chuantao Xie Chuantao Xie, Dana Cobzas, Julien Cohen-Adad, Jorge Corral Acero, Sujit Kumar Das, Marcela de Oliveira, Hanqiu Deng, Guiming Dong, Lars Doorenbos, Cory Efird, Sergio Escalera, Di Fan, Mehdi Fatan Serj, Alexandre Fenneteau, Lucas Fidon, Patryk Filipiak, René Finzel, Nuno R. Freitas, Christoph M. Friedrich, Mitchell Fulton, Finn Gaida, Francesco Galati, Christoforos Galazis, Chang Hee Gan, Zheyao Gao, Shengbo Gao, Matej Gazda, Beerend Gerats, Neil Getty, Adam Gibicar, Ryan Gifford, Sajan Gohil, Maria Grammatikopoulou, Daniel Grzech, Orhun Güley, Timo Günnemann, Chunxu Guo, Sylvain Guy, Heonjin Ha, Luyi Han, Il Song Han, Ali Hatamizadeh, Tian He, Jimin Heo, Sebastian Hitziger, SeulGi Hong, Seungbum Hong, Rian Huang, Ziyan Huang, Markus Huellebrand, Stephan Huschauer, Mustaffa Hussain, Tomoo Inubushi, Ece Isik Polat, Mojtaba Jafaritadi, SeongHun Jeong, Bailiang Jian, Yuanhong Jiang, Zhifan Jiang, Yueming Jin, Smriti Joshi, Abdolrahim Kadkhodamohammadi, Reda Abdellah Kamraoui, Inha Kang, Junghwa Kang, Davood Karimi, April Khademi, Muhammad Irfan Khan, Suleiman A. Khan, Rishab Khantwal, Kwang-Ju Kim, Timothy Kline, Satoshi Kondo, Elina Kontio, Adrian Krenzer, Artem Kroviakov, Hugo Kuijf, Satyadwyoom Kumar, Francesco La Rosa, Abhi Lad, Doohee Lee, Minho Lee, Chiara Lena, Hao Li, Ling Li, Xingyu Li, Fuyuan Liao, Kuanlun Liao, Arlindo Limede Oliveira, Chaonan Lin, Shan Lin, Akis Linardos, Marius George Linguraru, Han Liu, Tao Liu, Di Liu, Yanling Liu, João Lourenço-Silva, Jingpei Lu, Jiangshan Lu, Imanol Luengo, Christina B. Lund, Huan Minh Luu, Yi Lv, Uzay Macar, Leon Maechler, Sina Mansour L., Kenji Marshall, Moona Mazher, Richard McKinley, Alfonso Medela, Felix Meissen, Mingyuan Meng, Dylan Miller, Seyed Hossein Mirjahanmardi, Arnab Mishra, Samir Mitha, Hassan Mohy-ud-Din, Tony Chi Wing Mok, Gowtham Krishnan Murugesan, Enamundram Naga Karthik, Sahil Nalawade, Jakub Nalepa, Mohamed Naser, Ramin Nateghi, Hammad Naveed, Quang-Minh Nguyen, Cuong Nguyen Quoc, Brennan Nichyporuk, Bruno Oliveira, David Owen, Jimut Bahan Pal, Junwen Pan, Wentao Pan, Winnie Pang, Bogyu Park, Vivek Pawar, Kamlesh Pawar, Michael Peven, Lena Philipp, Tomasz Pieciak, Szymon Plotka, Marcel Plutat, Fattaneh Pourakpour, Domen Preložnik, Kumaradevan Punithakumar, Abdul Qayyum, Sandro Queirós, Arman Rahmim, Salar Razavi, Jintao Ren, Mina Rezaei, Jonathan Adam Rico, ZunHyan Rieu, Markus Rink, Johannes Roth, Yusely Ruiz-Gonzalez, Numan Saeed, Anindo Saha, Mostafa Salem, Ricardo Sanchez-Matilla, Kurt Schilling, Wei Shao, Zhiqiang Shen, Ruize Shi, Pengcheng Shi, Daniel Sobotka, Théodore Soulier, Bella Specktor Fadida, Danail Stoyanov, Timothy Sum Hon Mun, Xiaowu Sun, Rong Tao, Franz Thaler, Antoine Théberge, Felix Thielke, Helena Torres, Kareem A. Wahid, Jiacheng Wang, Yifei Wang, Wei Wang, Xiong Wang, Jianhui Wen, Ning Wen, Marek Wodzinski, Ye Wu, Fangfang Xia, Tianqi Xiang, Chen Xiaofei, Lizhan Xu, Tingting Xue, Yuxuan Yang, Lin Yang, Kai Yao, Huifeng Yao, Amirsaeed Yazdani, Michael Yip, Hwanseung Yoo, Fereshteh Yousefirizi, Shunkai Yu, Lei Yu, Jonathan Zamora, Ramy Ashraf Zeineldin, Dewen Zeng, Jianpeng Zhang, Bokai Zhang, Jiapeng Zhang, Fan Zhang, Huahong Zhang, Zhongchen Zhao, Zixuan Zhao, Jiachen Zhao, Can Zhao, Qingshuo Zheng, Yuheng Zhi, Ziqi Zhou, Baosheng Zou, Klaus Maier-Hein, Paul F. Jäger, Annette Kopp-Schneider, Lena Maier-Hein

Of these, 84% were based on standard architectures.

Benchmarking

Medical Diffusion: Denoising Diffusion Probabilistic Models for 3D Medical Image Generation

1 code implementation7 Nov 2022 Firas Khader, Gustav Mueller-Franzes, Soroosh Tayebi Arasteh, Tianyu Han, Christoph Haarburger, Maximilian Schulze-Hagen, Philipp Schad, Sandy Engelhardt, Bettina Baessler, Sebastian Foersch, Johannes Stegmaier, Christiane Kuhl, Sven Nebelung, Jakob Nikolas Kather, Daniel Truhn

Furthermore, we demonstrate that synthetic images can be used in a self-supervised pre-training and improve the performance of breast segmentation models when data is scarce (dice score 0. 91 vs. 0. 95 without vs. with synthetic data).

Computed Tomography (CT) Denoising +3

Self-supervised motion descriptor for cardiac phase detection in 4D CMR based on discrete vector field estimations

1 code implementation13 Sep 2022 Sven Koehler, Tarique Hussain, Hamza Hussain, Daniel Young, Samir Sarikouch, Thomas Pickhardt, Gerald Greil, Sandy Engelhardt

Simultaneously, deep learning-based deformable image registration is able to estimate discrete vector fields which warp one time step of a CMR sequence to the following in a self-supervised manner.

Image Registration

mvHOTA: A multi-view higher order tracking accuracy metric to measure spatial and temporal associations in multi-point detection

1 code implementation19 Jun 2022 Lalith Sharan, Halvar Kelm, Gabriele Romano, Matthias Karck, Raffaele De Simone, Sandy Engelhardt

The main evaluation metric available comes from Multi-object tracking (MOT) methods to benchmark performance on datasets such as KITTI with the recently proposed higher order tracking accuracy (HOTA) metric, which is capable of providing a better description of the performance over metrics such as MOTA, DetA, and IDF1.

Multi-Object Tracking object-detection +2

Posterior temperature optimized Bayesian models for inverse problems in medical imaging

1 code implementation2 Feb 2022 Max-Heinrich Laves, Malte Tölle, Alexander Schlaefer, Sandy Engelhardt

In POTOBIM, we optimize both the parameters of the prior distribution and the posterior temperature with respect to reconstruction accuracy using Bayesian optimization with Gaussian process regression.

Bayesian Optimization Image Denoising +1

Comparison of Evaluation Metrics for Landmark Detection in CMR Images

4 code implementations25 Jan 2022 Sven Koehler, Lalith Sharan, Julian Kuhm, Arman Ghanaat, Jelizaveta Gordejeva, Nike K. Simon, Niko M. Grell, Florian André, Sandy Engelhardt

In this work, we extended the public ACDC dataset with additional labels of the right ventricular insertion points and compare different variants of a heatmap-based landmark detection pipeline.

Point detection through multi-instance deep heatmap regression for sutures in endoscopy

1 code implementation16 Nov 2021 Lalith Sharan, Gabriele Romano, Julian Brand, Halvar Kelm, Matthias Karck, Raffaele De Simone, Sandy Engelhardt

Method: In this work, we formulate the suture detection task as a multi-instance deep heatmap regression problem, to identify entry and exit points of sutures.

regression

Mutually improved endoscopic image synthesis and landmark detection in unpaired image-to-image translation

1 code implementation14 Jul 2021 Lalith Sharan, Gabriele Romano, Sven Koehler, Halvar Kelm, Matthias Karck, Raffaele De Simone, Sandy Engelhardt

In this use case, it is of paramount importance to display objects like needles, sutures or instruments consistent in both domains while altering the style to a more tissue-like appearance.

Translation Unsupervised Image-To-Image Translation

Common Limitations of Image Processing Metrics: A Picture Story

1 code implementation12 Apr 2021 Annika Reinke, Minu D. Tizabi, Carole H. Sudre, Matthias Eisenmann, Tim Rädsch, Michael Baumgartner, Laura Acion, Michela Antonelli, Tal Arbel, Spyridon Bakas, Peter Bankhead, Arriel Benis, Matthew Blaschko, Florian Buettner, M. Jorge Cardoso, Jianxu Chen, Veronika Cheplygina, Evangelia Christodoulou, Beth Cimini, Gary S. Collins, Sandy Engelhardt, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Ben Glocker, Patrick Godau, Robert Haase, Fred Hamprecht, Daniel A. Hashimoto, Doreen Heckmann-Nötzel, Peter Hirsch, Michael M. Hoffman, Merel Huisman, Fabian Isensee, Pierre Jannin, Charles E. Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Alan Karthikesalingam, A. Emre Kavur, Hannes Kenngott, Jens Kleesiek, Andreas Kleppe, Sven Kohler, Florian Kofler, Annette Kopp-Schneider, Thijs Kooi, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A. Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L. Martel, Peter Mattson, Erik Meijering, Bjoern Menze, David Moher, Karel G. M. Moons, Henning Müller, Brennan Nichyporuk, Felix Nickel, M. Alican Noyan, Jens Petersen, Gorkem Polat, Susanne M. Rafelski, Nasir Rajpoot, Mauricio Reyes, Nicola Rieke, Michael Riegler, Hassan Rivaz, Julio Saez-Rodriguez, Clara I. Sánchez, Julien Schroeter, Anindo Saha, M. Alper Selver, Lalith Sharan, Shravya Shetty, Maarten van Smeden, Bram Stieltjes, Ronald M. Summers, Abdel A. Taha, Aleksei Tiulpin, Sotirios A. Tsaftaris, Ben van Calster, Gaël Varoquaux, Manuel Wiesenfarth, Ziv R. Yaniv, Paul Jäger, Lena Maier-Hein

While the importance of automatic image analysis is continuously increasing, recent meta-research revealed major flaws with respect to algorithm validation.

Instance Segmentation object-detection +2

How well do U-Net-based segmentation trained on adult cardiac magnetic resonance imaging data generalise to rare congenital heart diseases for surgical planning?

2 code implementations10 Feb 2020 Sven Koehler, Animesh Tandon, Tarique Hussain, Heiner Latus, Thomas Pickardt, Samir Sarikouch, Philipp Beerbaum, Gerald Greil, Sandy Engelhardt, Ivo Wolf

Our results confirm that current deep learning models can achieve excellent results (left ventricle dice of $0. 951\pm{0. 003}$/$0. 941\pm{0. 007}$ train/validation) within a single data collection.

Towards Augmented Reality-based Suturing in Monocular Laparoscopic Training

no code implementations19 Jan 2020 Chandrakanth Jayachandran Preetha, Jonathan Kloss, Fabian Siegfried Wehrtmann, Lalith Sharan, Carolyn Fan, Beat Peter Müller-Stich, Felix Nickel, Sandy Engelhardt

Reliable 3D localization of needle and instruments in real time could be used to augment the scene with additional parameters that describe their quantitative geometric relation, e. g. the relation between the estimated needle plane and its rotation center and the instrument.

Depth Estimation Segmentation

Improving Surgical Training Phantoms by Hyperrealism: Deep Unpaired Image-to-Image Translation from Real Surgeries

no code implementations10 Jun 2018 Sandy Engelhardt, Raffaele De Simone, Peter M. Full, Matthias Karck, Ivo Wolf

Though, application of this approach to continuous video frames can result in flickering, which turned out to be especially prominent for this application.

Computers and Society

Automatic Cardiac Disease Assessment on cine-MRI via Time-Series Segmentation and Domain Specific Features

1 code implementation3 Jul 2017 Fabian Isensee, Paul Jaeger, Peter M. Full, Ivo Wolf, Sandy Engelhardt, Klaus H. Maier-Hein

We evaluated our method on the ACDC dataset (4 pathology groups, 1 healthy group) and achieve dice scores of 0. 945 (LVC), 0. 908 (RVC) and 0. 905 (LVM) in a cross-validation over the training set (100 cases) and 0. 950 (LVC), 0. 923 (RVC) and 0. 911 (LVM) on the test set (50 cases).

General Classification Segmentation +3

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