publications

2025

1. 

   Learned, uncertainty-driven adaptive acquisition for photon-efficient scanning microscopy

   Cassandra Tong Ye, Jiashu Han, Kunzan Liu, and 4 more authors

   Optics Express, 2025

   Bib PDF Code Website

   @article{ye2025uncertainty,
     title = {Learned, uncertainty-driven adaptive acquisition for photon-efficient scanning microscopy},
     author = {Ye, Cassandra Tong and Han, Jiashu and Liu, Kunzan and Angelopoulos, Anastasios and Griffith, Linda and Monakhova, Kristina and You, Sixian},
     journal = {Optics Express},
     volume = {33},
     number = {6},
     pages = {12269-12287},
     year = {2025},
     publisher = {Optica Publishing Group},
   }

2. 

   System- and sample-agnostic isotropic three-dimensional microscopy by weakly physics-informed, domain-shift-resistant axial deblurring

   Jiashu Han Han, Kunzan Liu, Keith B. Isaacson, and 3 more authors

   Nature Communications, 2025

   Bib PDF Code Website

   @article{han2025system,
     title = {System- and sample-agnostic isotropic three-dimensional microscopy by weakly physics-informed, domain-shift-resistant axial deblurring},
     author = {Han, Jiashu Han and Liu, Kunzan and Isaacson, Keith B. and Monakhova, Kristina and G., Griffith Linda and You, Sixian},
     journal = {Nature Communications},
     year = {2025},
     publisher = {Nature},
   }

2023

1. 

   Roadmap on Deep Learning for Microscopy

   Giovanni Volpe, Carolina Wählby, Lei Tian, and 8 more authors

   ArXiv, 2023

   Bib PDF

   @article{volpe2023roadmap,
     title = {Roadmap on Deep Learning for Microscopy},
     author = {Volpe, Giovanni and W{\"a}hlby, Carolina and Tian, Lei and Hecht, Michael and Yakimovich, Artur and Monakhova, Kristina and Waller, Laura and Sbalzarini, Ivo F and Metzler, Christopher A and Xie, Mingyang and others},
     journal = {ArXiv},
     year = {2023},
     publisher = {arXiv},
   }

2022

1. 

   Physics-Informed Machine Learning for Computational Imaging

   Kristina Monakhova

   2022

   PDF

2. Dancing under the stars: video denoising in starlight

   Kristina Monakhova, Stephan R Richter, Laura Waller, and 1 more author

   In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 2022

   Bib PDF Code Website

   @inproceedings{monakhova2022dancing,
     title = {Dancing under the stars: video denoising in starlight},
     author = {Monakhova, Kristina and Richter, Stephan R and Waller, Laura and Koltun, Vladlen},
     booktitle = {Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition},
     pages = {16241--16251},
     year = {2022},
     video = {https://www.youtube.com/watch?v=eFvQs2j9RMw},
   }

3. 

   Deep learning for fast spatially varying deconvolution

   Kyrollos Yanny, Kristina Monakhova, Richard W Shuai, and 1 more author

   Optica, 2022

   Bib PDF Code Website

   @article{yanny2022deep,
     title = {Deep learning for fast spatially varying deconvolution},
     author = {Yanny, Kyrollos and Monakhova, Kristina and Shuai, Richard W and Waller, Laura},
     journal = {Optica},
     volume = {9},
     number = {1},
     pages = {96--99},
     year = {2022},
     publisher = {Optical Society of America},
   }

2021

1. 

   Untrained networks for compressive lensless photography

   Kristina Monakhova, Vi Tran, Grace Kuo, and 1 more author

   Optics Express, 2021

   Bib PDF Code Website

   @article{monakhova2021untrained,
     title = {Untrained networks for compressive lensless photography},
     author = {Monakhova, Kristina and Tran, Vi and Kuo, Grace and Waller, Laura},
     journal = {Optics Express},
     volume = {29},
     number = {13},
     pages = {20913--20929},
     year = {2021},
     publisher = {Optica Publishing Group},
   }

2020

1. 

   Spectral DiffuserCam: lensless snapshot hyperspectral imaging with a spectral filter array

   Kristina Monakhova, Kyrollos Yanny, Neerja Aggarwal, and 1 more author

   Optica, 2020

   Bib PDF Code Website

   @article{monakhova2020spectral,
     title = {Spectral DiffuserCam: lensless snapshot hyperspectral imaging with a spectral filter array},
     author = {Monakhova, Kristina and Yanny, Kyrollos and Aggarwal, Neerja and Waller, Laura},
     journal = {Optica},
     volume = {7},
     number = {10},
     pages = {1298--1307},
     year = {2020},
     publisher = {Optica Publishing Group},
     group = {journal},
   }

2. 

   Miniscope3D: optimized single-shot miniature 3D fluorescence microscopy

   Kyrollos Yanny, Nick Antipa, William Liberti, and 6 more authors

   Light: Science & Applications, 2020

   Bib PDF Code Website

   @article{yanny2020miniscope3d,
     title = {Miniscope3D: optimized single-shot miniature 3D fluorescence microscopy},
     author = {Yanny, Kyrollos and Antipa, Nick and Liberti, William and Dehaeck, Sam and Monakhova, Kristina and Liu, Fanglin Linda and Shen, Konlin and Ng, Ren and Waller, Laura},
     journal = {Light: Science \& Applications},
     volume = {9},
     number = {1},
     pages = {171},
     year = {2020},
     publisher = {Nature Publishing Group UK London},
   }

2019

1. 

   Learned reconstructions for practical mask-based lensless imaging

   Kristina Monakhova, Joshua Yurtsever, Grace Kuo, and 3 more authors

   Optics express, 2019

   Bib PDF Code Website

   @article{monakhova2019learned,
     title = {Learned reconstructions for practical mask-based lensless imaging},
     author = {Monakhova, Kristina and Yurtsever, Joshua and Kuo, Grace and Antipa, Nick and Yanny, Kyrollos and Waller, Laura},
     journal = {Optics express},
     volume = {27},
     number = {20},
     pages = {28075--28090},
     year = {2019},
     publisher = {Optica Publishing Group},
   }