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1. Biomedical image analysis competitions: The state of current participation practice

Author

Eisenmann, Matthias, Reinke, Annika, Weru, Vivienn, Tizabi, Minu Dietlinde, Isensee, Fabian, Adler, Tim J., Godau, Patrick, Cheplygina, Veronika, Kozubek, Michal, Ali, Sharib, Gupta, Anubha, Kybic, Jan, Noble, Alison, de Solórzano, Carlos Ortiz, Pachade, Samiksha, Petitjean, Caroline, Sage, Daniel, Wei, Donglai, Wilden, Elizabeth, Alapatt, Deepak, Andrearczyk, Vincent, Baid, Ujjwal, Bakas, Spyridon, Balu, Niranjan, Bano, Sophia, Bawa, Vivek Singh, Bernal, Jorge, Bodenstedt, Sebastian, Casella, Alessandro, Choi, Jinwook, Commowick, Olivier, Daum, Marie, Depeursinge, Adrien, Dorent, Reuben, Egger, Jan, Eichhorn, Hannah, Engelhardt, Sandy, Ganz, Melanie, Girard, Gabriel, Hansen, Lasse, Heinrich, Mattias, Heller, Nicholas, Hering, Alessa, Huaulmé, Arnaud, Kim, Hyunjeong, Landman, Bennett, Li, Hongwei Bran, Li, Jianning, Ma, Jun, Martel, Anne, Martín-Isla, Carlos, Menze, Bjoern, Nwoye, Chinedu Innocent, Oreiller, Valentin, Padoy, Nicolas, Pati, Sarthak, Payette, Kelly, Sudre, Carole, van Wijnen, Kimberlin, Vardazaryan, Armine, Vercauteren, Tom, Wagner, Martin, Wang, Chuanbo, Yap, Moi Hoon, Yu, Zeyun, Yuan, Chun, Zenk, Maximilian, Zia, Aneeq, Zimmerer, David, Bao, Rina, Choi, Chanyeol, Cohen, Andrew, Dzyubachyk, Oleh, Galdran, Adrian, Gan, Tianyuan, Guo, Tianqi, Gupta, Pradyumna, Haithami, Mahmood, Ho, Edward, Jang, Ikbeom, Li, Zhili, Luo, Zhengbo, Lux, Filip, Makrogiannis, Sokratis, Müller, Dominik, Oh, Young-tack, Pang, Subeen, Pape, Constantin, Polat, Gorkem, Reed, Charlotte Rosalie, Ryu, Kanghyun, Scherr, Tim, Thambawita, Vajira, Wang, Haoyu, Wang, Xinliang, Xu, Kele, Yeh, Hung, Yeo, Doyeob, Yuan, Yixuan, Zeng, Yan, Zhao, Xin, Abbing, Julian, Adam, Jannes, Adluru, Nagesh, Agethen, Niklas, Ahmed, Salman, Khalil, Yasmina Al, Alenyà, Mireia, Alhoniemi, Esa, An, Chengyang, Anwar, Talha, Arega, Tewodros Weldebirhan, Avisdris, Netanell, Aydogan, Dogu Baran, Bai, Yingbin, Calisto, Maria Baldeon, Basaran, Berke Doga, Beetz, Marcel, Bian, Cheng, Bian, Hao, Blansit, Kevin, Bloch, Louise, Bohnsack, Robert, Bosticardo, Sara, Breen, Jack, Brudfors, Mikael, Brüngel, Raphael, Cabezas, Mariano, Cacciola, Alberto, Chen, Zhiwei, Chen, Yucong, Chen, Daniel Tianming, Cho, Minjeong, Choi, Min-Kook, Xie, Chuantao Xie Chuantao, Cobzas, Dana, Cohen-Adad, Julien, Acero, Jorge Corral, Das, Sujit Kumar, de Oliveira, Marcela, Deng, Hanqiu, Dong, Guiming, Doorenbos, Lars, Efird, Cory, Escalera, Sergio, Fan, Di, Serj, Mehdi Fatan, Fenneteau, Alexandre, Fidon, Lucas, Filipiak, Patryk, Finzel, René, Freitas, Nuno R., Friedrich, Christoph M., Fulton, Mitchell, Gaida, Finn, Galati, Francesco, Galazis, Christoforos, Gan, Chang Hee, Gao, Zheyao, Gao, Shengbo, Gazda, Matej, Gerats, Beerend, Getty, Neil, Gibicar, Adam, Gifford, Ryan, Gohil, Sajan, Grammatikopoulou, Maria, Grzech, Daniel, Güley, Orhun, Günnemann, Timo, Guo, Chunxu, Guy, Sylvain, Ha, Heonjin, Han, Luyi, Han, Il Song, Hatamizadeh, Ali, He, Tian, Heo, Jimin, Hitziger, Sebastian, Hong, SeulGi, Hong, SeungBum, Huang, Rian, Huang, Ziyan, Huellebrand, Markus, Huschauer, Stephan, Hussain, Mustaffa, Inubushi, Tomoo, Polat, Ece Isik, Jafaritadi, Mojtaba, Jeong, SeongHun, Jian, Bailiang, Jiang, Yuanhong, Jiang, Zhifan, Jin, Yueming, Joshi, Smriti, Kadkhodamohammadi, Abdolrahim, Kamraoui, Reda Abdellah, Kang, Inha, Kang, Junghwa, Karimi, Davood, Khademi, April, Khan, Muhammad Irfan, Khan, Suleiman A., Khantwal, Rishab, Kim, Kwang-Ju, Kline, Timothy, Kondo, Satoshi, Kontio, Elina, Krenzer, Adrian, Kroviakov, Artem, Kuijf, Hugo, Kumar, Satyadwyoom, La Rosa, Francesco, Lad, Abhi, Lee, Doohee, Lee, Minho, Lena, Chiara, Li, Hao, Li, Ling, Li, Xingyu, Liao, Fuyuan, Liao, KuanLun, Oliveira, Arlindo Limede, Lin, Chaonan, Lin, Shan, Linardos, Akis, Linguraru, Marius George, Liu, Han, Liu, Tao, Liu, Di, Liu, Yanling, Lourenço-Silva, João, Lu, Jingpei, Lu, Jiangshan, Luengo, Imanol, Lund, Christina B., Luu, Huan Minh, Lv, Yi, Macar, Uzay, Maechler, Leon, L., Sina Mansour, Marshall, Kenji, Mazher, Moona, McKinley, Richard, Medela, Alfonso, Meissen, Felix, Meng, Mingyuan, Miller, Dylan, Mirjahanmardi, Seyed Hossein, Mishra, Arnab, Mitha, Samir, Mohy-ud-Din, Hassan, Mok, Tony Chi Wing, Murugesan, Gowtham Krishnan, Karthik, Enamundram Naga, Nalawade, Sahil, Nalepa, Jakub, Naser, Mohamed, Nateghi, Ramin, Naveed, Hammad, Nguyen, Quang-Minh, Quoc, Cuong Nguyen, Nichyporuk, Brennan, Oliveira, Bruno, Owen, David, Pal, Jimut Bahan, Pan, Junwen, Pan, Wentao, Pang, Winnie, Park, Bogyu, Pawar, Vivek, Pawar, Kamlesh, Peven, Michael, Philipp, Lena, Pieciak, Tomasz, Plotka, Szymon, Plutat, Marcel, Pourakpour, Fattaneh, Preložnik, Domen, Punithakumar, Kumaradevan, Qayyum, Abdul, Queirós, Sandro, Rahmim, Arman, Razavi, Salar, Ren, Jintao, Rezaei, Mina, Rico, Jonathan Adam, Rieu, ZunHyan, Rink, Markus, Roth, Johannes, Ruiz-Gonzalez, Yusely, Saeed, Numan, Saha, Anindo, Salem, Mostafa, Sanchez-Matilla, Ricardo, Schilling, Kurt, Shao, Wei, Shen, Zhiqiang, Shi, Ruize, Shi, Pengcheng, Sobotka, Daniel, Soulier, Théodore, Fadida, Bella Specktor, Stoyanov, Danail, Mun, Timothy Sum Hon, Sun, Xiaowu, Tao, Rong, Thaler, Franz, Théberge, Antoine, Thielke, Felix, Torres, Helena, Wahid, Kareem A., Wang, Jiacheng, Wang, YiFei, Wang, Wei, Wang, Xiong, Wen, Jianhui, Wen, Ning, Wodzinski, Marek, Wu, Ye, Xia, Fangfang, Xiang, Tianqi, Xiaofei, Chen, Xu, Lizhan, Xue, Tingting, Yang, Yuxuan, Yang, Lin, Yao, Kai, Yao, Huifeng, Yazdani, Amirsaeed, Yip, Michael, Yoo, Hwanseung, Yousefirizi, Fereshteh, Yu, Shunkai, Yu, Lei, Zamora, Jonathan, Zeineldin, Ramy Ashraf, Zeng, Dewen, Zhang, Jianpeng, Zhang, Bokai, Zhang, Jiapeng, Zhang, Fan, Zhang, Huahong, Zhao, Zhongchen, Zhao, Zixuan, Zhao, Jiachen, Zhao, Can, Zheng, Qingshuo, Zhi, Yuheng, Zhou, Ziqi, Zou, Baosheng, Maier-Hein, Klaus, Jäger, Paul F., Kopp-Schneider, Annette, and Maier-Hein, Lena

Subjects
Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning
Abstract

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps.

Published
2022

2. ModDrop++: A Dynamic Filter Network with Intra-subject Co-training for Multiple Sclerosis Lesion Segmentation with Missing Modalities

Author

Liu, Han, Fan, Yubo, Li, Hao, Wang, Jiacheng, Hu, Dewei, Cui, Can, Lee, Ho Hin, Zhang, Huahong, and Oguz, Ipek

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition
Abstract

Multiple Sclerosis (MS) is a chronic neuroinflammatory disease and multi-modality MRIs are routinely used to monitor MS lesions. Many automatic MS lesion segmentation models have been developed and have reached human-level performance. However, most established methods assume the MRI modalities used during training are also available during testing, which is not guaranteed in clinical practice. Previously, a training strategy termed Modality Dropout (ModDrop) has been applied to MS lesion segmentation to achieve the state-of-the-art performance with missing modality. In this paper, we present a novel method dubbed ModDrop++ to train a unified network adaptive to an arbitrary number of input MRI sequences. ModDrop++ upgrades the main idea of ModDrop in two key ways. First, we devise a plug-and-play dynamic head and adopt a filter scaling strategy to improve the expressiveness of the network. Second, we design a co-training strategy to leverage the intra-subject relation between full modality and missing modality. Specifically, the intra-subject co-training strategy aims to guide the dynamic head to generate similar feature representations between the full- and missing-modality data from the same subject. We use two public MS datasets to show the superiority of ModDrop++. Source code and trained models are available at https://github.com/han-liu/ModDropPlusPlus., Comment: MICCAI 2022

Published
2022

3. Unsupervised Cross-Modality Domain Adaptation for Segmenting Vestibular Schwannoma and Cochlea with Data Augmentation and Model Ensemble

Author

Li, Hao, Hu, Dewei, Zhu, Qibang, Larson, Kathleen E., Zhang, Huahong, and Oguz, Ipek

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition
Abstract

Magnetic resonance images (MRIs) are widely used to quantify vestibular schwannoma and the cochlea. Recently, deep learning methods have shown state-of-the-art performance for segmenting these structures. However, training segmentation models may require manual labels in target domain, which is expensive and time-consuming. To overcome this problem, domain adaptation is an effective way to leverage information from source domain to obtain accurate segmentations without requiring manual labels in target domain. In this paper, we propose an unsupervised learning framework to segment the VS and cochlea. Our framework leverages information from contrast-enhanced T1-weighted (ceT1-w) MRIs and its labels, and produces segmentations for T2-weighted MRIs without any labels in the target domain. We first applied a generator to achieve image-to-image translation. Next, we ensemble outputs from an ensemble of different models to obtain final segmentations. To cope with MRIs from different sites/scanners, we applied various 'online' augmentations during training to better capture the geometric variability and the variability in image appearance and quality. Our method is easy to build and produces promising segmentations, with a mean Dice score of 0.7930 and 0.7432 for VS and cochlea respectively in the validation set.

Published
2021

4. Multiple Sclerosis Lesion Segmentation -- A Survey of Supervised CNN-Based Methods

Author

Zhang, Huahong and Oguz, Ipek

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning
Abstract

Lesion segmentation is a core task for quantitative analysis of MRI scans of Multiple Sclerosis patients. The recent success of deep learning techniques in a variety of medical image analysis applications has renewed community interest in this challenging problem and led to a burst of activity for new algorithm development. In this survey, we investigate the supervised CNN-based methods for MS lesion segmentation. We decouple these reviewed works into their algorithmic components and discuss each separately. For methods that provide evaluations on public benchmark datasets, we report comparisons between their results., Comment: Accepted by BrainLes 2020

Published
2020

5. Unsupervised Cross-modality Domain Adaptation for Segmenting Vestibular Schwannoma and Cochlea with Data Augmentation and Model Ensemble

Author

Li, Hao, Hu, Dewei, Zhu, Qibang, Larson, Kathleen E., Zhang, Huahong, Oguz, Ipek, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Crimi, Alessandro, editor, and Bakas, Spyridon, editor

Published
2022
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7. Generalizing MRI Subcortical Segmentation to Neurodegeneration

Author

Li, Hao, Zhang, Huahong, Hu, Dewei, Johnson, Hans, Long, Jeffrey D., Paulsen, Jane S., Oguz, Ipek, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Kia, Seyed Mostafa, editor, Mohy-ud-Din, Hassan, editor, Abdulkadir, Ahmed, editor, Bass, Cher, editor, Habes, Mohamad, editor, Rondina, Jane Maryam, editor, Tax, Chantal, editor, Wang, Hongzhi, editor, Wolfers, Thomas, editor, Rathore, Saima, editor, and Ingalhalikar, Madhura, editor

Published
2020
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8. Robust Multiple Sclerosis Lesion Inpainting with Edge Prior

Author

Zhang, Huahong, Bakshi, Rohit, Bagnato, Francesca, Oguz, Ipek, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Liu, Mingxia, editor, Yan, Pingkun, editor, Lian, Chunfeng, editor, and Cao, Xiaohuan, editor

Published
2020
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11. Multiple Sclerosis Lesion Segmentation with Tiramisu and 2.5D Stacked Slices

Author

Zhang, Huahong, Valcarcel, Alessandra M., Bakshi, Rohit, Chu, Renxin, Bagnato, Francesca, Shinohara, Russell T., Hett, Kilian, Oguz, Ipek, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Shen, Dinggang, editor, Liu, Tianming, editor, Peters, Terry M., editor, Staib, Lawrence H., editor, Essert, Caroline, editor, Zhou, Sean, editor, Yap, Pew-Thian, editor, and Khan, Ali, editor

Published
2019
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21. The Model Technology of Stepping Motor Driving System

Author

Zhang Huahong

Subjects
History, Basis (linear algebra), Computer science, System identification, Optimal control, Motion (physics), Computer Science Applications, Education, Control theory, Value (economics), Numerical control, Stepper motor, MATLAB, computer, computer.programming_language
Abstract

This paper proposes the dynamic characteristics of load motion have great influence on the performance of stepping motor. The dynamic model of stepping motor driving system is established on basis of least-squares, the system identification experiment is carried out on an actual Numerical Control Plate Printer drive system, and the dynamic parameters of the system were identified with MATLAB. The results have a good practical value to the optimal control of stepping motor.

Published
2019

28. Astragaloside IV promotes the pyroptosis of airway smooth muscle cells in childhood asthma by suppressing HMGB1/RAGE axis to inactivate NF-κb pathway.

Author

Zhang H, Zhang J, Pan H, Yang K, and Hu C

Subjects
Animals, Mice, Humans, Disease Models, Animal, Saponins pharmacology, Pyroptosis drug effects, HMGB1 Protein metabolism, Myocytes, Smooth Muscle metabolism, Myocytes, Smooth Muscle drug effects, NF-kappa B metabolism, Asthma drug therapy, Asthma metabolism, Asthma pathology, Triterpenes pharmacology, Receptor for Advanced Glycation End Products metabolism, Signal Transduction drug effects
Abstract

Childhood asthma, a common chronic childhood disease, leads to high mortality and morbidity in the world. Airway smooth muscle cells (ASMCs) is a group of multifunctional cells that has been found to be correlated with the pathogenesis of asthma. Astragaloside IV (AS-IV) is a compound extracted from Astragalus membranaceus , which has the anti-asthmatic effect. However, the role of molecular mechanisms regulated by AS-IV in the biological processes of ASMCs in asthma remains unclear. Our current study aims to investigate the downstream molecular mechanism of AS-IV in modulating the aberrant proliferation and pyroptosis of ASMCs in asthma. At first, we determined that the viability of ASMCs could be efficiently suppressed by AS-IV treatment (200 μM). Moreover, AS-IV promoted the pyroptosis and suppressed PDGF-BB-induced aberrant proliferation. Through mechanism investigation, we confirmed that AS-IV could suppress high mobility group box 1 (HMGB1) expression and prevent it from entering the cytoplasm. Subsequently, AS-IV blocked the interaction between HMGB1 and advanced glycosylation end product-specific receptor (RAGE) to inactivate NF-κB pathway. Finally, in vivo experiments demonstrated that AS-IV treatment can alleviate the lung inflammation in asthma mice. Collectively, AS-IV alleviates asthma and suppresses the pyroptosis of AMSCs through blocking HMGB1/RAGE axis to inactivate NF-κB pathway.

Published
2024
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29. MRI subcortical segmentation in neurodegeneration with cascaded 3D CNNs.

Author

Li H, Zhang H, Johnson H, Long JD, Paulsen JS, and Oguz I

Abstract

The subcortical structures of the brain are relevant for many neurodegenerative diseases like Huntington's disease (HD). Quantitative segmentation of these structures from magnetic resonance images (MRIs) has been studied in clinical and neuroimaging research. Recently, convolutional neural networks (CNNs) have been successfully used for many medical image analysis tasks, including subcortical segmentation. In this work, we propose a 2-stage cascaded 3D subcortical segmentation framework, with the same 3D CNN architecture for both stages. Attention gates, residual blocks and output adding are used in our proposed 3D CNN. In the first stage, we apply our model to downsampled images to output a coarse segmentation. Next, we crop the extended subcortical region from the original image based on this coarse segmentation, and we input the cropped region to the second CNN to obtain the final segmentation. Left and right pairs of thalamus, caudate, pallidum and putamen are considered in our segmentation. We use the Dice coefficient as our metric and evaluate our method on two datasets: the publicly available IBSR dataset and a subset of the PREDICT-HD database, which includes healthy controls and HD subjects. We train our models on only healthy control subjects and test on both healthy controls and HD subjects to examine model generalizability. Compared with the state-of-the-art methods, our method has the highest mean Dice score on all considered subcortical structures (except the thalamus on IBSR), with more pronounced improvement for HD subjects. This suggests that our method may have better ability to segment MRIs of subjects with neurodegenerative disease.

Published
2021
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30. Longitudinal subcortical segmentation with deep learning.

Author

Li H, Zhang H, Johnson H, Long JD, Paulsen JS, and Oguz I

Abstract

Longitudinal information is important for monitoring the progression of neurodegenerative diseases, such as Huntington's disease (HD). Specifically, longitudinal magnetic resonance imaging (MRI) studies may allow the discovery of subtle intra-subject changes over time that may otherwise go undetected because of inter-subject variability. For HD patients, the primary imaging-based marker of disease progression is the atrophy of subcortical structures, mainly the caudate and putamen. To better understand the course of subcortical atrophy in HD and its correlation with clinical outcome measures, highly accurate segmentation is important. In recent years, subcortical segmentation methods have moved towards deep learning, given the state-of-the-art accuracy and computational efficiency provided by these models. However, these methods are not designed for longitudinal analysis, but rather treat each time point as an independent sample, discarding the longitudinal structure of the data. In this paper, we propose a deep learning based subcortical segmentation method that takes into account this longitudinal information. Our method takes a longitudinal pair of 3D MRIs as input, and jointly computes the corresponding segmentations. We use bi-directional convolutional long short-term memory (C-LSTM) blocks in our model to leverage the longitudinal information between scans. We test our method on the PREDICT-HD dataset and use the Dice coefficient, average surface distance and 95-percent Hausdorff distance as our evaluation metrics. Compared to cross-sectional segmentation, we improve the overall accuracy of segmentation, and our method has more consistent performance across time points. Furthermore, our method identifies a stronger correlation between subcortical volume loss and decline in the total motor score, an important clinical outcome measure for HD.

Published
2021
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