Publications

2024

1. 

   Modality-Specific Strategies for Medical Image Segmentation using Lightweight SAM Architectures

   Thuy T. Dao* ,  Xincheng Ye* ,  Joshua Scarsbrook , and 3 more authors

   In CVPR 2024: Segment Anything In Medical Images On Laptop , 2024

   Bib Code

   @inproceedings{dao2024modalityspecific,
     title = {Modality-Specific Strategies for Medical Image Segmentation using Lightweight {SAM} Architectures},
     author = {Dao*, Thuy T. and Ye*, Xincheng and Scarsbrook, Joshua and Balarupan, Gowrienanthan and Ribeiro, Fernanda Lenita and Bollmann, Steffen},
     booktitle = {CVPR 2024: Segment Anything In Medical Images On Laptop},
     year = {2024},
     url = {https://openreview.net/forum?id=bEQ2KJ9Cgw}
   }

2. 

   Neurodesk: An accessible, flexible, and portable data analysis environment for reproducible neuroimaging

   Angela I. Renton* ,  Thuy T. Dao* ,  Tom Johnstone , and 45 more authors

   Nature Methods, Jan 2024

   Abs Bib Code

   Neuroimaging data analysis often requires purpose-built software, which can be challenging to install and may produce different results across computing environments. Beyond being a roadblock to neuroscientists, these issues of accessibility and portability can hamper the reproducibility of neuroimaging data analysis pipelines. Here, we introduce the Neurodesk platform, which harnesses software containers to support a comprehensive and growing suite of neuroimaging software (https://www.neurodesk.org/). Neurodesk includes a browser-accessible virtual desktop environment and a command line interface, mediating access to containerized neuroimaging software libraries on various computing platforms, including personal and high-performance computers, cloud computing and Jupyter Notebooks. This community-oriented, open-source platform enables a paradigm shift for neuroimaging data analysis, allowing for accessible, flexible, fully reproducible, and portable data analysis pipelines.Competing Interest StatementThe authors have declared no competing interest.

   @article{renton_neurodesk_2023,
     title = {Neurodesk: {An} accessible, flexible, and portable data analysis environment for reproducible neuroimaging},
     url = {https://doi.org/10.1038/s41592-023-02145-x},
     doi = {10.1038/s41592-023-02145-x},
     journal = {Nature Methods},
     author = {Renton*, Angela I. and Dao*, Thuy T. and Johnstone, Tom and Civier, Oren and Sullivan, Ryan P. and White, David J. and Lyons, Paris and Slade, Benjamin M. and Abbott, David F. and Amos, Toluwani J. and Bollmann, Saskia and Botting, Andy and Campbell, Megan E. J. and Chang, Jeryn and Close, Thomas G. and Eckstein, Korbinian and Egan, Gary F. and Evas, Stefanie and Flandin, Guillaume and Garner, Kelly G. and Garrido, Marta I. and Ghosh, Satrajit S. and Grignard, Martin and Hannan, Anthony J. and Huber, Renzo and Kaczmarzyk, Jakub R. and Kasper, Lars and Kuhlmann, Levin and Lou, Kexin and Mantilla-Ramos, Yorguin-Jose and Mattingley, Jason B. and Morris, Jo and Narayanan, Akshaiy and Pestilli, Franco and Puce, Aina and Ribeiro, Fernanda L. and Rogasch, Nigel C. and Rorden, Chris and Schira, Mark and Shaw, Thomas B. and Sowman, Paul F. and Spitz, Gershon and Stewart, Ashley and Ye, Xincheng and Zhu, Judy D. and Hughes, Matthew E. and Narayanan, Aswin and Bollmann, Steffen},
     month = jan,
     year = {2024},
   }

2023

1. 

   Developing a secure, browser-based and interactive image segmentation system for medical images

   Thuy T. Dao ,  Chris Rorden ,  Korbinian Eckstein , and 3 more authors

   Jan 2023

   Bib

   @conference{dao_niivue_2023,
     title = {Developing a secure, browser-based and interactive image segmentation system for medical images},
     year = {2023},
     author = {Dao, Thuy T. and Rorden, Chris and Eckstein, Korbinian and Haehn, Daniel and Varade, Shruti and Bollmann, Steffen},
     organization = {International Society for Magnetic Resonance in Medicine ANZ Chapter},
   }

2. 

   Investigating the computational reproducibility of Neurodesk

   Thuy T. Dao ,  Angela Renton ,  Aswin Narayanan , and 2 more authors

   Jan 2023

   Bib

   @conference{dao_neurodesk_2023,
     title = {Investigating the computational reproducibility of Neurodesk},
     author = {Dao, Thuy T. and Renton, Angela and Narayanan, Aswin and Barth, Markus and Bollmann, Steffen},
     year = {2023},
     organization = {International Society for Magnetic Resonance in Medicine},
   }

3. 

   Proceedings of the OHBM Brainhack 2021

   Aki Nikolaidis ,  Matteo Manchini ,  Tibor Auer , and 97 more authors

   Aperture Neuro, Mar 2023

   Bib

   @article{Nikolaidis2023,
     title = {Proceedings of the OHBM Brainhack 2021},
     url = {http://dx.doi.org/10.52294/258801b4-a9a9-4d30-a468-c43646391211},
     doi = {10.52294/258801b4-a9a9-4d30-a468-c43646391211},
     journal = {Aperture Neuro},
     publisher = {Organization for Human Brain Mapping},
     author = {Nikolaidis, Aki and Manchini, Matteo and Auer, Tibor and L. Bottenhorn, Katherine and Alonso-Ortiz, Eva and Gonzalez-Escamilla, Gabriel and Valk, Sofie and Glatard, Tristan and Selim Atay, Melvin and M.M. Bayer, Johanna and Bijsterbosch, Janine and Algermissen, Johannes and Beck, Natacha and Bermudez, Patrick and Poyraz Bilgin, Isil and Bollmann, Steffen and Bradley, Claire and E.J. Campbell, Megan and Caron, Bryan and Civier, Oren and Pedro Coelho, Luis and El Damaty, Shady and Das, Samir and Dugré, Mathieu and Earl, Eric and Evas, Stefanie and Lopes Fischer, Nastassja and Fu Yap, De and G. Garner, Kelly and Gau, Remi and Ganis, Giorgio and G. E. Gomes, Dylan and Grignard, Martin and Guay, Samuel and Faruk Gulban, Omer and Hamburg, Sarah and O. Halchenko, Yaroslav and Hayot-Sasson, Valerie and Liu Holford, Dawn and Huber, Laurentius and Illanes, Manuel and Johnstone, Tom and Kalyani, Avinash and Kashyap, Kinshuk and Ke, Han and Khormi, Ibrahim and Kiar, Gregory and Ković, Vanja and Kuehn, Tristan and Kumar, Achintya and Lecours-Boucher, Xavier and L\"{u}hrs, Michael and Luke, Robert and Madjar, Cecile and Mansour L., Sina and Markeweicz, Chris and Andrea Martinez, Paula and McCarroll, Alexandra and Michel, Léa and Moia, Stefano and Narayanan, Aswin and Niso, Guiomar and A. O’Brien, Emmet and Oudyk, Kendra and Paugam, Fran\c{c}ois and G. Pavlov, Yuri and Poline, Jean-Baptiste and A. Poser, Benedikt and Provins, Céline and Reddy Raamana, Pradeep and Rioux, Pierre and Romero-Bascones, David and Sareen, Ekansh and Schettino, Antonio and Shaw, Alec and Shaw, Thomas and A. Smout, Cooper and Šoškié, Anđdela and Stone, Jessica and J Styles, Suzy and Sullivan, Ryan and Sunami, Naoyuki and Sundaray, Shamala and Wei Rou, Jasmine and Thanh Thuy, Dao and Tourbier, Sebastien and Urch, Sebastián and de la Vega, Alejandro and Viswarupan, Niruhan and Wagner, Adina and Walger, Lennart and Wang, Hao-Ting and Ting Woon, Fei and White, David and Wiggins, Christopher and Woods, Will and Yang, Yu-Fang and Zaytseva, Ksenia and D. Zhu, Judy and P. Zwiers, Marcel},
     year = {2023},
     month = mar,
   }

2021

1. 

   A possible mechanism of earthquake-induced landslides focusing on pulse-like ground motions

   Guangqi Chen ,  Mingyao Xia ,  Thuy T. Dao , and 1 more author

   Landslides, Jan 2021

   https://link.springer.com/article/10.1007/s10346-020-01597-y

   Bib

   @article{chen_xia_thuy_zhang_2021,
     title = {A possible mechanism of earthquake-induced landslides focusing on pulse-like ground motions},
     volume = {18},
     doi = {10.1007/s10346-020-01597-y},
     number = {5},
     journal = {Landslides},
     author = {Chen, Guangqi and Xia, Mingyao and Dao, Thuy T. and Zhang, Yingbin},
     year = {2021},
     month = jan,
     pages = {1641–1657},
     note = {https://link.springer.com/article/10.1007/s10346-020-01597-y}
   }