Publications

Emma Alexander; Leyla A Kabuli; Oliver S Cossairt; Laura Waller

Depth from Defocus as a Special Case of the Transport of Intensity Equation Proceedings Article

In: 2021 IEEE International Conference on Computational Photography (ICCP), pp. 1-13, 2021.

Links | BibTeX | Tags: coherence, fluorescence imaging, phase imaging

Kyrollos Yanny; Nick Antipa; William Liberti; Sam Dehaeck; Kristina Monakhova; Fanglin Linda Liu; Konlin Shen; Ren Ng; Laura Waller

Miniscope3D: optimized single-shot miniature 3D fluorescence microscopy Journal Article

In: Light: Science & Applications, vol. 9, no. 171, 2020.

Abstract | Links | BibTeX | Tags: 3D imaging, algorithms, diffuser, fluorescence imaging

@article{yanny2020,

title = {Miniscope3D: optimized single-shot miniature 3D fluorescence microscopy},

author = {Kyrollos Yanny and Nick Antipa and William Liberti and Sam Dehaeck and Kristina Monakhova and Fanglin Linda Liu and Konlin Shen and Ren Ng and Laura Waller},

url = {https://www.nature.com/articles/s41377-020-00403-7},

doi = {https://doi.org/10.1038/s41377-020-00403-7},

year  = {2020},

date = {2020-10-02},

journal = {Light: Science & Applications},

volume = {9},

number = {171},

abstract = {Miniature fluorescence microscopes are a standard tool in systems biology. However, widefield miniature microscopes capture only 2D information, and modifications that enable 3D capabilities increase the size and weight and have poor resolution outside a narrow depth range. Here, we achieve the 3D capability by replacing the tube lens of a conventional 2D Miniscope with an optimized multifocal phase mask at the objective’s aperture stop. Placing the phase mask at the aperture stop significantly reduces the size of the device, and varying the focal lengths enables a uniform resolution across a wide depth range. The phase mask encodes the 3D fluorescence intensity into a single 2D measurement, and the 3D volume is recovered by solving a sparsity-constrained inverse problem. We provide methods for designing and fabricating the phase mask and an efficient forward model that accounts for the field-varying aberrations in miniature objectives. We demonstrate a prototype that is 17 mm tall and weighs 2.5 grams, achieving 2.76 μm lateral, and 15 μm axial resolution across most of the 900 × 700 × 390 μm3 volume at 40 volumes per second. The performance is validated experimentally on resolution targets, dynamic biological samples, and mouse brain tissue. Compared with existing miniature single-shot volume-capture implementations, our system is smaller and lighter and achieves a more than 2× better lateral and axial resolution throughout a 10× larger usable depth range. Our microscope design provides single-shot 3D imaging for applications where a compact platform matters, such as volumetric neural imaging in freely moving animals and 3D motion studies of dynamic samples in incubators and lab-on-a-chip devices.},

keywords = {3D imaging, algorithms, diffuser, fluorescence imaging},

pubstate = {published},

tppubtype = {article}

}

Grace Kuo; Fanglin Linda Liu; Irene Grossrubatscher; Ren Ng; Laura Waller

On-chip fluorescence microscopy with a random microlens diffuser Journal Article

In: Optics Express, vol. 28, no. 6, pp. 8384–8399, 2020.

Links | BibTeX | Tags: 3D imaging, diffuser, fluorescence imaging, lensless imaging, on-chip

Kevin Zhang; Michael Kellman; Emrah Bostan; Laura Waller

3D fluorescence deconvolution with deep priors Proceedings Article

In: Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXVII, pp. 112450N, International Society for Optics and Photonics 2020.

BibTeX | Tags: 3D imaging, deconvolution, fluorescence imaging, learning-based