RT-utils: A Minimal Python Library for RT-struct Manipulation.

Carlos F. Uribe

Asim Shrestha Adam Watkins Fereshteh Yousefirizi Arman Rahmim Carlos F. Uribe RT-utils: A Minimal Python Library for RT-struct Manipulation. 7361 2025 May 10 J. Open Source Softw. 109 https://doi.org/10.21105/joss.07361 db/journals/jossw/jossw10.html#ShresthaWYRU25 streams/journals/jossw

Lucas A. Polson Roberto Fedrigo Chenguang Li Maziar Sabouri Obed Dzikunu Shadab Ahamed Nicolas A. Karakatsanis Sara Kurkowska Peyman Sheikhzadeh Pedro L. Esquinas Arman Rahmim Carlos F. Uribe PyTomography: A python library for medical image reconstruction. 102020 2025 29 SoftwareX https://doi.org/10.1016/j.softx.2024.102020 db/journals/softx/softx29.html#PolsonFLSDAKKSERU25 streams/journals/softx

Lucas A. Polson Sara Kurkowska Chenguang Li Pedro L. Esquinas Peyman Sheikhzadeh Mehrshad Abbasi François Bénard Carlos F. Uribe Arman Rahmim Uncertainty Propagation From Projections to Region Counts in Tomographic Imaging: Application to Radiopharmaceutical Dosimetry. 3233-3244 2025 August 44 IEEE Trans. Medical Imaging 8 https://doi.org/10.1109/TMI.2025.3560330 db/journals/tmi/tmi44.html#PolsonKLESABUR25 streams/journals/tmi

Alejandro López-Montes Fereshteh Yousefirizi Yizhou Chen Yazdan Salimi Robert Seifert Ali Afshar-Oromieh Carlos F. Uribe Axel Rominger Habib Zaidi Arman Rahmim Kuangyu Shi Artificial intelligence for simplified patient-centered dosimetry in radiopharmaceutical therapies. 2025 October abs/2510.12714 CoRR https://doi.org/10.48550/arXiv.2510.12714 db/journals/corr/corr2510.html#abs-2510-12714 streams/journals/corr

Anahita Piranfar Madjid Soltani Farshad Moradi Kashkooli Carlos F. Uribe Arman Rahmim Spatiotemporal modeling of radiopharmaceutical transport in solid tumors: Application to 177Lu-PSMA therapy of prostate cancer. 108004 2024 245 Comput. Methods Programs Biomed. https://doi.org/10.1016/j.cmpb.2023.108004 db/journals/cmpb/cmpb245.html#PiranfarSKUR24

Obed Dzikunu Maziar Sabouri Shadab Ahamed Carlos F. Uribe Arman Rahmim Lucas A. Polson SlicerSPECTRecon: A 3D Slicer Extension for SPECT Image Reconstruction. 7399 2024 December 9 J. Open Source Softw. 104 https://doi.org/10.21105/joss.07399 db/journals/jossw/jossw9.html#DzikunuSAURP24 streams/journals/jossw

Maziar Sabouri Shadab Ahamed Azin Asadzadeh Atlas Haddadi Avval Soroush Bagheri Mohsen Arabi Seyed Rasoul Zakavi Emran Askari Ali Rasouli Atena Aghaee Mohaddese Sehati Fereshteh Yousefirizi Carlos F. Uribe Ghasem Hajianfar Habib Zaidi Arman Rahmim Thyroidiomics: An Automated Pipeline for Segmentation and Classification of Thyroid Pathologies from Scintigraphy Images. 1-6 2024 EUVIP https://doi.org/10.1109/EUVIP61797.2024.10772785 conf/euvip/2024 db/conf/euvip/euvip2024.html#SabouriAAABAZARASYUHZR24 streams/conf/euvip Amirhosein Toosi Sara Harsini François Bénard Carlos F. Uribe Arman Rahmim How to Segment in 3D Using 2D Models: Automated 3D Segmentation of Prostate Cancer Metastatic Lesions on PET Volumes Using Multi-angle Maximum Intensity Projections and Diffusion Models. 212-221 2024 DGM4MICCAI@MICCAI https://doi.org/10.1007/978-3-031-72744-3_21 conf/miccai/2024dgm4miccai db/conf/miccai/dgm4miccai2024.html#ToosiHBUR24 streams/conf/miccai

Shadab Ahamed Yixi Xu Ingrid Bloise Joo H. O Carlos F. Uribe Rahul Dodhia Juan Lavista Ferres Arman Rahmim A slice classification neural network for automated classification of axial PET/CT slices from a multi-centric lymphoma dataset. 2024 abs/2403.07105 CoRR https://doi.org/10.48550/arXiv.2403.07105 db/journals/corr/corr2403.html#abs-2403-07105

Amirhosein Toosi Sara Harsini François Bénard Carlos F. Uribe Arman Rahmim How To Segment in 3D Using 2D Models: Automated 3D Segmentation of Prostate Cancer Metastatic Lesions on PET Volumes Using Multi-Angle Maximum Intensity Projections and Diffusion Models. 2024 abs/2407.18555 CoRR https://doi.org/10.48550/arXiv.2407.18555 db/journals/corr/corr2407.html#abs-2407-18555 streams/journals/corr

Yixi Xu Ivan S. Klyuzhin Sara Harsini Anthony Ortiz Shun Zhang François Bénard Rahul Dodhia Carlos F. Uribe Arman Rahmim Juan Lavista Ferres Automatic segmentation of prostate cancer metastases in PSMA PET/CT images using deep neural networks with weighted batch-wise dice loss. 106882 2023 May 158 Comput. Biol. Medicine https://doi.org/10.1016/j.compbiomed.2023.106882 db/journals/cbm/cbm158.html#XuKHOZBDURF23

Shadab Ahamed Yixi Xu Ingrid Bloise Joo Hyun O Carlos F. Uribe Rahul Dodhia Juan Lavista Ferres Arman Rahmim A slice classification neural network for automated classification of axial PET/CT slices from a multi-centric lymphoma dataset. 2023 Image Processing https://doi.org/10.1117/12.2652947 conf/miip/2023 db/conf/miip/miip2023.html#AhamedXBOUDFR23 Amirhosein Toosi Sara Harsini Shadab Ahamed Fereshteh Yousefirizi François Bénard Carlos F. Uribe Arman Rahmim State-of-the-art object detection algorithms for small lesion detection in PSMA PET: use of rotational maximum intensity projection (MIP) images. 2023 Image Processing https://doi.org/10.1117/12.2654527 conf/miip/2023 db/conf/miip/miip2023.html#ToosiHAYBUR23 Fereshteh Yousefirizi Joo Hyun O Ingrid Bloise Amirhosein Toosi Carlos F. Uribe Arman Rahmim Revisiting the supervision level in semi-supervised learning for automated tumor segmentation: application to lymphoma FDG PET imaging. 2023 Image Processing https://doi.org/10.1117/12.2654492 conf/miip/2023 db/conf/miip/miip2023.html#YousefiriziOBTU23 Roberto Fedrigo Fereshteh Yousefirizi Ziping Liu Abhinav K. Jha Robert V. Bergen Jean-François Rajotte Raymond T. Ng Ingrid Bloise Sara Harsini Dan J. Kadrmas Carlos F. Uribe Arman Rahmim Observer study-based evaluation of TGAN architecture used to generate oncological PET images. 2023 Image Perception, Observer Performance, and Technology Assessment https://doi.org/10.1117/12.2652661 conf/miipop/2023 db/conf/miipop/miipop2023.html#FedrigoYLJBRNBH23

Shadab Ahamed Yixi Xu Claire Gowdy Joo Hyun O Ingrid Bloise Don Wilson Patrick Martineau François Bénard Fereshteh Yousefirizi Rahul Dodhia Juan M. Lavista Ferres William B. Weeks Carlos F. Uribe Arman Rahmim Comprehensive Evaluation and Insights into the Use of Deep Neural Networks to Detect and Quantify Lymphoma Lesions in PET/CT Images. 2023 abs/2311.09614 CoRR https://doi.org/10.48550/arXiv.2311.09614 db/journals/corr/corr2311.html#abs-2311-09614

Shadab Ahamed Natalia Dubljevic Ingrid Bloise Claire Gowdy Patrick Martineau Don Wilson Carlos F. Uribe Arman Rahmim Fereshteh Yousefirizi A cascaded deep network for automated tumor detection and segmentation in clinical PET imaging of diffuse large B-cell lymphoma. 2022 Image Processing https://doi.org/10.1117/12.2612684 conf/miip/2022 db/conf/miip/miip2022.html#AhamedDBGMWURY22 Fereshteh Yousefirizi Natalia Dubljevic Shadab Ahamed Ingrid Bloise Claire Gowdy Joo Hyun O Youssef Farag Rodrigue de Schaetzen Patrick Martineau Don Wilson Carlos F. Uribe Arman Rahmim Convolutional neural network with a hybrid loss function for fully automated segmentation of lymphoma lesions in FDG PET images. 2022 Image Processing https://doi.org/10.1117/12.2612675 conf/miip/2022 db/conf/miip/miip2022.html#YousefiriziDABG22

Arman Rahmim Amirhosein Toosi Mohammad R. Salmanpour Natalia Dubljevic Ian Janzen Isaac Shiri Mohamad A. Ramezani Ren Yuan Cheryl Ho Habib Zaidi Calum MacAulay Carlos F. Uribe Fereshteh Yousefirizi Tensor Radiomics: Paradigm for Systematic Incorporation of Multi-Flavoured Radiomics Features. 2022 abs/2203.06314 CoRR https://doi.org/10.48550/arXiv.2203.06314 db/journals/corr/corr2203.html#abs-2203-06314

Mehrshad Abbasi Ali Afshar-Oromieh Atena Aghaee Shadab Ahamed Mohsen Arabi Azin Asadzadeh Emran Askari Atlas Haddadi Avval Soroush Bagheri François Bénard Robert V. Bergen Ingrid Bloise Yizhou Chen Rahul Dodhia Natalia Dubljevic Obed Dzikunu Pedro L. Esquinas Youssef Farag Roberto Fedrigo Juan Lavista FerresJuan M. Lavista Ferres Claire Gowdy Ghasem Hajianfar Sara Harsini Cheryl Ho Ian Janzen Abhinav K. Jha Dan J. Kadrmas Nicolas A. Karakatsanis Farshad Moradi Kashkooli Ivan S. Klyuzhin Sara Kurkowska Chenguang Li Ziping Liu Alejandro López-Montes Calum MacAulay Patrick Martineau Raymond T. Ng Joo H. O Joo Hyun O Anthony Ortiz Anahita Piranfar Lucas A. Polson Arman Rahmim Jean-François Rajotte Mohamad A. Ramezani Ali Rasouli Fereshteh Yousefi RiziFereshteh Yousefirizi Axel Rominger Maziar Sabouri Yazdan Salimi Mohammad R. Salmanpour Rodrigue de Schaetzen Mohaddese Sehati Robert Seifert Peyman Sheikhzadeh Kuangyu Shi Isaac Shiri Asim Shrestha Madjid Soltani Amirhosein Toosi Adam Watkins William B. Weeks Don Wilson Yixi Xu Ren Yuan Habib Zaidi Seyed Rasoul Zakavi Shun Zhang