Publications by Henry Pinkard
2026
Leyla A. Kabuli; Henry Pinkard; Eric Markley; Clara S. Hung; Laura Waller
Designing lensless imaging systems to maximize information capture Journal Article
In: Optica, vol. 13, no. 2, pp. 227–235, 2026.
@article{Kabuli:26,
title = {Designing lensless imaging systems to maximize information capture},
author = {Leyla A. Kabuli and Henry Pinkard and Eric Markley and Clara S. Hung and Laura Waller},
url = {https://opg.optica.org/optica/abstract.cfm?URI=optica-13-2-227},
doi = {10.1364/OPTICA.570334},
year = {2026},
date = {2026-02-01},
journal = {Optica},
volume = {13},
number = {2},
pages = {227–235},
publisher = {Optica Publishing Group},
abstract = {Mask-based lensless imaging uses an optical encoder (e.g., a phase or amplitude mask) to capture measurements, then a computational decoding algorithm to reconstruct images. In this work, we evaluate and design lensless encoders based on the information content of their measurements using mutual information estimation. Our approach formalizes the object-dependent nature of lensless imaging and quantifies the interdependence between object sparsity, encoder multiplexing, and noise. Our analysis reveals that optimal encoder designs should tailor encoder multiplexing to object sparsity for maximum information capture, and that all optimally encoded measurements share the same level of sparsity. Using mutual information-based optimization, we design information-optimal encoders for compressive imaging of fixed object distributions. Our designs demonstrate improved downstream reconstruction performance for objects in the distribution, without requiring joint optimization with a specific reconstruction algorithm. We validate our approach experimentally by evaluating lensless imaging systems directly from captured measurements, without the need for image formation models, reconstruction algorithms, or ground truth data. Our comprehensive analysis establishes design and engineering principles for lensless imaging systems and offers a model for the study of general multiplexing systems, especially those with object-dependent performance.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Mask-based lensless imaging uses an optical encoder (e.g., a phase or amplitude mask) to capture measurements, then a computational decoding algorithm to reconstruct images. In this work, we evaluate and design lensless encoders based on the information content of their measurements using mutual information estimation. Our approach formalizes the object-dependent nature of lensless imaging and quantifies the interdependence between object sparsity, encoder multiplexing, and noise. Our analysis reveals that optimal encoder designs should tailor encoder multiplexing to object sparsity for maximum information capture, and that all optimally encoded measurements share the same level of sparsity. Using mutual information-based optimization, we design information-optimal encoders for compressive imaging of fixed object distributions. Our designs demonstrate improved downstream reconstruction performance for objects in the distribution, without requiring joint optimization with a specific reconstruction algorithm. We validate our approach experimentally by evaluating lensless imaging systems directly from captured measurements, without the need for image formation models, reconstruction algorithms, or ground truth data. Our comprehensive analysis establishes design and engineering principles for lensless imaging systems and offers a model for the study of general multiplexing systems, especially those with object-dependent performance.
2022
Henry Pinkard; Laura Waller
Microscopes are coming for your job Journal Article
In: Nature Methods, pp. 1–2, 2022.
@article{pinkard2022microscopes,
title = {Microscopes are coming for your job},
author = {Henry Pinkard and Laura Waller},
url = {https://www.nature.com/articles/s41592-022-01566-4},
year = {2022},
date = {2022-09-08},
urldate = {2022-01-01},
journal = {Nature Methods},
pages = {1--2},
publisher = {Nature Publishing Group},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2021
Henry Pinkard; Hratch Baghdassarian; Adriana Mujal; Ed Roberts; Kenneth H Hu; Daniel Haim Friedman; Ivana Malenica; Taylor Shagam; Adam Fries; Kaitlin Corbin; others
Learned adaptive multiphoton illumination microscopy for large-scale immune response imaging Journal Article
In: Nature communications, vol. 12, no. 1, pp. 1–14, 2021.
@article{pinkard2021learned,
title = {Learned adaptive multiphoton illumination microscopy for large-scale immune response imaging},
author = {Henry Pinkard and Hratch Baghdassarian and Adriana Mujal and Ed Roberts and Kenneth H Hu and Daniel Haim Friedman and Ivana Malenica and Taylor Shagam and Adam Fries and Kaitlin Corbin and others},
doi = {https://doi.org/10.1038/s41467-021-22246-5},
year = {2021},
date = {2021-01-01},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {1--14},
publisher = {Nature Publishing Group},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Henry Pinkard; Nico Stuurman; Ivan E Ivanov; Nicholas M Anthony; Wei Ouyang; Bin Li; Bin Yang; Mark A Tsuchida; Bryant Chhun; Grace Zhang; others
Pycro-Manager: open-source software for customized and reproducible microscope control Journal Article
In: Nature Methods, vol. 18, no. 3, pp. 226–228, 2021.
@article{pinkard2021pycro,
title = {Pycro-Manager: open-source software for customized and reproducible microscope control},
author = {Henry Pinkard and Nico Stuurman and Ivan E Ivanov and Nicholas M Anthony and Wei Ouyang and Bin Li and Bin Yang and Mark A Tsuchida and Bryant Chhun and Grace Zhang and others},
doi = {https://doi.org/10.1038/s41592-021-01087-6},
year = {2021},
date = {2021-01-01},
journal = {Nature Methods},
volume = {18},
number = {3},
pages = {226--228},
publisher = {Nature Publishing Group},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2019
Henry Pinkard; Zachary F Phillips; Arman Babakhani; Daniel A Fletcher; Laura Waller
Deep learning for single-shot autofocus microscopy Journal Article
In: Optica, vol. 6, no. 6, pp. 794–797, 2019.
@article{pinkard2019deep,
title = {Deep learning for single-shot autofocus microscopy},
author = { Henry Pinkard and Zachary F Phillips and Arman Babakhani and Daniel A Fletcher and Laura Waller},
url = {https://www.osapublishing.org/optica/abstract.cfm?uri=optica-6-6-794},
year = {2019},
date = {2019-06-20},
journal = {Optica},
volume = {6},
number = {6},
pages = {794--797},
publisher = {Optical Society of America},
keywords = {},
pubstate = {published},
tppubtype = {article}
}