Publications by Shwetadwip Chowdhury
2020
Michael Chen; David Ren; Hsiou-Yuan Liu; Shwetadwip Chowdhury; Laura Waller
Multi-layer Born multiple-scattering model for 3D phase microscopy Journal Article
In: Optica, vol. 7, no. 5, pp. 394–403, 2020.
@article{Chen:20,
title = {Multi-layer Born multiple-scattering model for 3D phase microscopy},
author = {Michael Chen and David Ren and Hsiou-Yuan Liu and Shwetadwip Chowdhury and Laura Waller},
url = {http://www.osapublishing.org/optica/abstract.cfm?URI=optica-7-5-394},
doi = {10.1364/OPTICA.383030},
year = {2020},
date = {2020-05-01},
journal = {Optica},
volume = {7},
number = {5},
pages = {394--403},
publisher = {OSA},
abstract = {We propose an accurate and computationally efficient 3D scattering model, multi-layer Born (MLB), and use it to recover the 3D refractive index (RI) of thick biological samples. For inverse problems recovering the complex field of thick samples, weak scattering models (e.g., first Born) may fail or underestimate the RI, especially with a large index contrast. Multi-slice (MS) beam propagation methods model multiple scattering to provide more realistic reconstructions; however, MS does not properly account for highly oblique scattering, nor does it model backward scattering. Our proposed MLB model uses a first Born model at each of many slices, accurately capturing the oblique scattering effects and estimating the backward scattering process. When used in conjunction with an inverse solver, the model provides more accurate RI reconstructions for high-resolution phase tomography. Importantly, MLB retains a reasonable computation time that is critical for practical implementation with iterative inverse algorithms.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We propose an accurate and computationally efficient 3D scattering model, multi-layer Born (MLB), and use it to recover the 3D refractive index (RI) of thick biological samples. For inverse problems recovering the complex field of thick samples, weak scattering models (e.g., first Born) may fail or underestimate the RI, especially with a large index contrast. Multi-slice (MS) beam propagation methods model multiple scattering to provide more realistic reconstructions; however, MS does not properly account for highly oblique scattering, nor does it model backward scattering. Our proposed MLB model uses a first Born model at each of many slices, accurately capturing the oblique scattering effects and estimating the backward scattering process. When used in conjunction with an inverse solver, the model provides more accurate RI reconstructions for high-resolution phase tomography. Importantly, MLB retains a reasonable computation time that is critical for practical implementation with iterative inverse algorithms.
2019
Matthew Wells; Jesus Deloya Garcia; Shwetadwip Chowdhury; Michael Kellman; Laura Waller; Rachel Pepper
Characterizing the feeding current of sessile microorganisms using digital holography Inproceedings
In: APS Division of Fluid Dynamics , 2019.
@inproceedings{wells2019characterizing,
title = {Characterizing the feeding current of sessile microorganisms using digital holography},
author = { Matthew Wells and Jesus Deloya Garcia and Shwetadwip Chowdhury and Michael Kellman and Laura Waller and Rachel Pepper},
url = {https://ui.adsabs.harvard.edu/abs/2019APS..DFDN05082W/abstract},
year = {2019},
date = {2019-11-01},
booktitle = {APS Division of Fluid Dynamics },
journal = {APS},
volume = {Fall 2019},
number = {NP05--082},
abstract = {Microscopic sessile suspension feeders (MSSFs) are single-celled organisms that live attached to surfaces in freshwater and marine environments. MSSFs generate a feeding current to consume bacteria and debris. They play a vital role in aquatic ecosystems of moving carbon up the food chain. Therefore, characterizing MSSF feeding flow is important for understanding their role in the environment. MSSF feeding flows have only been viewed in 2D and often with samples pressed between two coverslips that distort the flow. However, calculations predict the feeding current forms recirculating eddies when the MSSF body is oriented perpendicular to the surface of attachment. These eddies reduce feeding rate, and as the MSSF tends toward a parallel orientation it is predicted that the eddies disappear. Here we test those predictions by measuring 3D flow around individual Vorticella. Vorticellaare a common and representative MSSF. We use digital holography to record 3D videos of Vorticella in water seeded with 5-10 μm spherical flow tracers. We then use Particle Tracking Velocimetry to find fluid velocity from particle trajectories. },
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Microscopic sessile suspension feeders (MSSFs) are single-celled organisms that live attached to surfaces in freshwater and marine environments. MSSFs generate a feeding current to consume bacteria and debris. They play a vital role in aquatic ecosystems of moving carbon up the food chain. Therefore, characterizing MSSF feeding flow is important for understanding their role in the environment. MSSF feeding flows have only been viewed in 2D and often with samples pressed between two coverslips that distort the flow. However, calculations predict the feeding current forms recirculating eddies when the MSSF body is oriented perpendicular to the surface of attachment. These eddies reduce feeding rate, and as the MSSF tends toward a parallel orientation it is predicted that the eddies disappear. Here we test those predictions by measuring 3D flow around individual Vorticella. Vorticellaare a common and representative MSSF. We use digital holography to record 3D videos of Vorticella in water seeded with 5-10 μm spherical flow tracers. We then use Particle Tracking Velocimetry to find fluid velocity from particle trajectories.
Shwetadwip Chowdhury; Michael Chen; Regina Eckert; David Ren; Fan Wu; Nicole A Repina; Laura Waller
High-resolution 3D refractive index microscopy of multiple-scattering samples from intensity images Journal Article
In: Optica, vol. 6, no. 9, pp. 1211–1219, 2019.
@article{chowdhury2019high,
title = {High-resolution 3D refractive index microscopy of multiple-scattering samples from intensity images},
author = { Shwetadwip Chowdhury and Michael Chen and Regina Eckert and David Ren and Fan Wu and Nicole A Repina and Laura Waller},
url = {https://doi.org/10.1364/OPTICA.6.001211},
doi = {10.1364/OPTICA.6.001211},
year = {2019},
date = {2019-09-16},
journal = {Optica},
volume = {6},
number = {9},
pages = {1211--1219},
publisher = {Optical Society of America},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Li-Hao Yeh; Shwetadwip Chowdhury; Nicole A Repina; Laura Waller
Speckle-structured illumination for 3D phase and fluorescence computational microscopy Journal Article
In: Biomedical optics express, vol. 10, no. 7, pp. 3635–3653, 2019.
@article{yeh2019speckle,
title = {Speckle-structured illumination for 3D phase and fluorescence computational microscopy},
author = { Li-Hao Yeh and Shwetadwip Chowdhury and Nicole A Repina and Laura Waller},
url = {https://doi.org/10.1364/BOE.10.003635},
doi = {10.1364/BOE.10.003635},
year = {2019},
date = {2019-07-01},
journal = {Biomedical optics express},
volume = {10},
number = {7},
pages = {3635--3653},
publisher = {Optical Society of America},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Li-Hao Yeh; Shwetadwip Chowdhury; Laura Waller
Computational structured illumination for high-content fluorescence and phase microscopy Journal Article
In: Biomedical optics express, vol. 10, no. 4, pp. 1978–1998, 2019.
@article{yeh2019computational,
title = {Computational structured illumination for high-content fluorescence and phase microscopy},
author = { Li-Hao Yeh and Shwetadwip Chowdhury and Laura Waller},
url = {https://www.osapublishing.org/boe/abstract.cfm?uri=boe-10-4-1978
https://doi.org/10.1364/BOE.10.001978},
doi = {10.1364/BOE.10.001978},
year = {2019},
date = {2019-04-01},
journal = {Biomedical optics express},
volume = {10},
number = {4},
pages = {1978--1998},
publisher = {Optical Society of America},
abstract = {High-content biological microscopy targets high-resolution imaging across large fields-of-view (FOVs). Recent works have demonstrated that computational imaging can provide efficient solutions for high-content microscopy. Here, we use speckle structured illumination microscopy (SIM) as a robust and cost-effective solution for high-content fluorescence microscopy with simultaneous high-content quantitative phase (QP). This multi-modal compatibility is essential for studies requiring cross-correlative biological analysis. Our method uses laterally-translated Scotch tape to generate high-resolution speckle illumination patterns across a large FOV. Custom optimization algorithms then jointly reconstruct the sample’s super-resolution fluorescent (incoherent) and QP (coherent) distributions, while digitally correcting for system imperfections such as unknown speckle illumination patterns, system aberrations and pattern translations. Beyond previous linear SIM works, we achieve resolution gains of 4× the objective’s diffraction-limited native resolution, resulting in 700 nm fluorescence and 1.2 μm QP resolution, across a FOV of 2×2.7 mm 2, giving a space-bandwidth product (SBP) of 60 megapixels.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
High-content biological microscopy targets high-resolution imaging across large fields-of-view (FOVs). Recent works have demonstrated that computational imaging can provide efficient solutions for high-content microscopy. Here, we use speckle structured illumination microscopy (SIM) as a robust and cost-effective solution for high-content fluorescence microscopy with simultaneous high-content quantitative phase (QP). This multi-modal compatibility is essential for studies requiring cross-correlative biological analysis. Our method uses laterally-translated Scotch tape to generate high-resolution speckle illumination patterns across a large FOV. Custom optimization algorithms then jointly reconstruct the sample’s super-resolution fluorescent (incoherent) and QP (coherent) distributions, while digitally correcting for system imperfections such as unknown speckle illumination patterns, system aberrations and pattern translations. Beyond previous linear SIM works, we achieve resolution gains of 4× the objective’s diffraction-limited native resolution, resulting in 700 nm fluorescence and 1.2 μm QP resolution, across a FOV of 2×2.7 mm 2, giving a space-bandwidth product (SBP) of 60 megapixels.
2018
Shwetadwip Chowdhury; Regina Eckert; Michael Chen; Laura Waller
High-resolution 3D Phase Microscopy from Intensity Inproceedings
In: Microscopy Histopathology and Analytics, pp. MF3A–5, Optical Society of America 2018.
@inproceedings{chowdhury2018high,
title = {High-resolution 3D Phase Microscopy from Intensity},
author = { Shwetadwip Chowdhury and Regina Eckert and Michael Chen and Laura Waller},
url = {https://doi.org/10.1364/MICROSCOPY.2018.MF3A.5},
year = {2018},
date = {2018-04-03},
booktitle = {Microscopy Histopathology and Analytics},
pages = {MF3A--5},
organization = {Optical Society of America},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}