Developing Generalist Foundation Models from a Multimodal Dataset for 3D Computed Tomography

1 code implementation • 26 Mar 2024 • Ibrahim Ethem Hamamci, Sezgin Er, Furkan Almas, Ayse Gulnihan Simsek, Sevval Nil Esirgun, Irem Dogan, Muhammed Furkan Dasdelen, Omer Faruk Durugol, Bastian Wittmann, Tamaz Amiranashvili, Enis Simsar, Mehmet Simsar, Emine Bensu Erdemir, Abdullah Alanbay, Anjany Sekuboyina, Berkan Lafci, Christian Bluethgen, Mehmet Kemal Ozdemir, Bjoern Menze

By combining CT-CLIP's vision encoder with a pretrained large language model, we create CT-CHAT, a vision-language foundational chat model for 3D chest CT volumes.

Anomaly Detection Large Language Model +1

CT2Rep: Automated Radiology Report Generation for 3D Medical Imaging

1 code implementation • 11 Mar 2024 • Ibrahim Ethem Hamamci, Sezgin Er, Bjoern Menze

Medical imaging plays a crucial role in diagnosis, with radiology reports serving as vital documentation.

Benchmarking the CoW with the TopCoW Challenge: Topology-Aware Anatomical Segmentation of the Circle of Willis for CTA and MRA

2 code implementations • 29 Dec 2023 • Kaiyuan Yang, Fabio Musio, Yihui Ma, Norman Juchler, Johannes C. Paetzold, Rami Al-Maskari, Luciano Höher, Hongwei Bran Li, Ibrahim Ethem Hamamci, Anjany Sekuboyina, Suprosanna Shit, Houjing Huang, Chinmay Prabhakar, Ezequiel de la Rosa, Diana Waldmannstetter, Florian Kofler, Fernando Navarro, Martin Menten, Ivan Ezhov, Daniel Rueckert, Iris Vos, Ynte Ruigrok, Birgitta Velthuis, Hugo Kuijf, Julien Hämmerli, Catherine Wurster, Philippe Bijlenga, Laura Westphal, Jeroen Bisschop, Elisa Colombo, Hakim Baazaoui, Andrew Makmur, James Hallinan, Bene Wiestler, Jan S. Kirschke, Roland Wiest, Emmanuel Montagnon, Laurent Letourneau-Guillon, Adrian Galdran, Francesco Galati, Daniele Falcetta, Maria A. Zuluaga, Chaolong Lin, Haoran Zhao, Zehan Zhang, Sinyoung Ra, Jongyun Hwang, HyunJin Park, Junqiang Chen, Marek Wodzinski, Henning Müller, Pengcheng Shi, Wei Liu, Ting Ma, Cansu Yalçin, Rachika E. Hamadache, Joaquim Salvi, Xavier Llado, Uma Maria Lal-Trehan Estrada, Valeriia Abramova, Luca Giancardo, Arnau Oliver, Jialu Liu, Haibin Huang, Yue Cui, Zehang Lin, Yusheng Liu, Shunzhi Zhu, Tatsat R. Patel, Vincent M. Tutino, Maysam Orouskhani, Huayu Wang, Mahmud Mossa-Basha, Chengcheng Zhu, Maximilian R. Rokuss, Yannick Kirchhoff, Nico Disch, Julius Holzschuh, Fabian Isensee, Klaus Maier-Hein, Yuki Sato, Sven Hirsch, Susanne Wegener, Bjoern Menze

The TopCoW dataset was the first public dataset with voxel-level annotations for thirteen possible CoW vessel components, enabled by virtual-reality (VR) technology.

Anatomy Benchmarking +1

Synthesizing Missing MRI Sequences from Available Modalities using Generative Adversarial Networks in BraTS Dataset

no code implementations • 11 Oct 2023 • Ibrahim Ethem Hamamci

Glioblastoma is a highly aggressive and lethal form of brain cancer.

Brain Tumor Segmentation Diagnostic +1

DENTEX: An Abnormal Tooth Detection with Dental Enumeration and Diagnosis Benchmark for Panoramic X-rays

1 code implementation • 30 May 2023 • Ibrahim Ethem Hamamci, Sezgin Er, Enis Simsar, Atif Emre Yuksel, Sadullah Gultekin, Serife Damla Ozdemir, Kaiyuan Yang, Hongwei Bran Li, Sarthak Pati, Bernd Stadlinger, Albert Mehl, Mustafa Gundogar, Bjoern Menze

To address these issues, the Dental Enumeration and Diagnosis on Panoramic X-rays Challenge (DENTEX) has been organized in association with the International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI) in 2023.

GenerateCT: Text-Conditional Generation of 3D Chest CT Volumes

1 code implementation • 25 May 2023 • Ibrahim Ethem Hamamci, Sezgin Er, Anjany Sekuboyina, Enis Simsar, Alperen Tezcan, Ayse Gulnihan Simsek, Sevval Nil Esirgun, Furkan Almas, Irem Dogan, Muhammed Furkan Dasdelen, Chinmay Prabhakar, Hadrien Reynaud, Sarthak Pati, Christian Bluethgen, Mehmet Kemal Ozdemir, Bjoern Menze

GenerateCT, the first approach to generating 3D medical imaging conditioned on free-form medical text prompts, incorporates a text encoder and three key components: a novel causal vision transformer for encoding 3D CT volumes, a text-image transformer for aligning CT and text tokens, and a text-conditional super-resolution diffusion model.

Computed Tomography (CT) Image Generation +5

Diffusion-Based Hierarchical Multi-Label Object Detection to Analyze Panoramic Dental X-rays

2 code implementations • 11 Mar 2023 • Ibrahim Ethem Hamamci, Sezgin Er, Enis Simsar, Anjany Sekuboyina, Mustafa Gundogar, Bernd Stadlinger, Albert Mehl, Bjoern Menze

To learn from all three hierarchies jointly, we introduce a novel diffusion-based hierarchical multi-label object detection framework by adapting a diffusion-based method that formulates object detection as a denoising diffusion process from noisy boxes to object boxes.

Denoising Object +2

AutoCOR: Autonomous Condylar Offset Ratio Calculator on TKA-Postoperative Lateral Knee X-ray

no code implementations • 6 Apr 2022 • Gulsade Rabia Cakmak, Ibrahim Ethem Hamamci, Mehmet Kursat Yilmaz, Reda Alhajj, Ibrahim Azboy, Mehmet Kemal Ozdemir

The software AutoCOR is capable of detecting the anterior/posterior edge points and anterior/posterior cortex of the femoral shaft on true postoperative lateral conventional radiographs.