Programmable illumination control is essential for many computational microscopy techniques. Conventional light source array is often arranged on a fixed grid of a planar surface for providing programmable sample illumination. Here, we report the development of a freeform illuminator that can be arranged at arbitrary 2-dimensional or 3-dimensional (3D) surface structures for computational microscopy. The freeform illuminator can be designed in a small form factor with a dense light source arrangement in 3D. It can be placed closer to the sample for providing angle-varied illumination with higher optical flux and smaller angular increment. With the freeform illuminators, we develop a calibration process using a low-cost Raspberry-Pi image sensor coated with a monolayer of blood cells. By tracking the positional shift of the blood-cell diffraction patterns at 2 distinct regions of the coded sensor, we can infer the 3D positions of the light source elements in a way similar to the stereo vision reconstruction approach. To demonstrate the applications for computational microscopy, we validate the freeform illuminators for Fourier ptychographic microscopy, 3D tomographic imaging, and on-chip microscopy. We also present a longitudinal study by tracking the growth of live bacterial cultures over a large field of view. The reported freeform illuminators and the related calibration process offer flexibilities and extended scope for imaging innovations in computational microscopy.
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Optofluidic ptychography on a chip
We report the implementation of a fully on-chip, lensless microscopy technique termed optofluidic ptychography. This imaging modality complements the miniaturization provided by microfluidics and allows the integration of ptychographic microscopy into various lab-on-a-chip devices. In our prototype, we place a microfluidic channel on the top surface of a coverslip and coat the bottom surface with a scattering layer. The channel and the coated coverslip substrate are then placed on top of an image sensor for diffraction data acquisition. Similar to the operation of a flow cytometer, the device utilizes microfluidic flow to deliver specimens across the channel. The diffracted light from the flowing objects is modulated by the scattering layer and recorded by the image sensor for ptychographic reconstruction, where high-resolution quantitative complex images are recovered from the diffraction measurements. By using an image sensor with a 1.85 μm pixel size, our device can resolve the 550 nm linewidth on the resolution target. We validate the device by imaging different types of biospecimens, including C. elegans , yeast cells, paramecium , and closterium sp . We also demonstrate a high-resolution ptychographic reconstruction at a video framerate of 30 frames per second. The reported technique can address a wide range of biomedical needs and engenders new ptychographic imaging innovations in a flow cytometer configuration.
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- Award ID(s):
- 2012140
- NSF-PAR ID:
- 10335637
- Date Published:
- Journal Name:
- Lab on a Chip
- Volume:
- 21
- Issue:
- 23
- ISSN:
- 1473-0197
- Page Range / eLocation ID:
- 4549 to 4556
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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We report a novel lensless on-chip microscopy platform based on near-field blind ptychographic modulation. In this platform, we place a thin diffuser in between the object and the image sensor for light wave modulation. By blindly scanning the unknown diffuser to different x – y positions, we acquire a sequence of modulated intensity images for quantitative object recovery. Different from previous ptychographic implementations, we employ a unit magnification configuration with a Fresnel number of ∼50 000, which is orders of magnitude higher than those of previous ptychographic setups. The unit magnification configuration allows us to have the entire sensor area, 6.4 mm by 4.6 mm, as the imaging field of view. The ultra-high Fresnel number enables us to directly recover the positional shift of the diffuser in the phase retrieval process, addressing the positioning accuracy issue plaguing regular ptychographic experiments. In our implementation, we use a low-cost, DIY scanning stage to perform blind diffuser modulation. Precise mechanical scanning that is critical in conventional ptychography experiments is no longer needed in our setup. We further employ an up-sampling phase retrieval scheme to bypass the resolution limit set by the imager pixel size and demonstrate a half-pitch resolution of 0.78 μm. We validate the imaging performance via in vitro cell cultures, transparent and stained tissue sections, and a thick biological sample. We show that the recovered quantitative phase map can be used to perform effective cell segmentation of a dense yeast culture. We also demonstrate 3D digital refocusing of the thick biological sample based on the recovered wavefront. The reported platform provides a cost-effective and turnkey solution for large field-of-view, high-resolution, and quantitative on-chip microscopy. It is adaptable for a wide range of point-of-care-, global-health-, and telemedicine-related applications.more » « less
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We present a tomographic imaging technique, termed Deep Prior Diffraction Tomography (DP-DT), to reconstruct the 3D refractive index (RI) of thick biological samples at high resolution from a sequence of low-resolution images collected under angularly varying illumination. DP-DT processes the multi-angle data using a phase retrieval algorithm that is extended by a deep image prior (DIP), which reparameterizes the 3D sample reconstruction with an untrained, deep generative 3D convolutional neural network (CNN). We show that DP-DT effectively addresses the missing cone problem, which otherwise degrades the resolution and quality of standard 3D reconstruction algorithms. As DP-DT does not require pre-captured data or pre-training, it is not biased towards any particular dataset. Hence, it is a general technique that can be applied to a wide variety of 3D samples, including scenarios in which large datasets for supervised training would be infeasible or expensive. We applied DP-DT to obtain 3D RI maps of bead phantoms and complex biological specimens, both in simulation and experiment, and show that DP-DT produces higher-quality results than standard regularization techniques. We further demonstrate the generality of DP-DT, using two different scattering models, the first Born and multi-slice models. Our results point to the potential benefits of DP-DT for other 3D imaging modalities, including X-ray computed tomography, magnetic resonance imaging, and electron microscopy.
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Fourier ptychographic microscopy is a computational imaging technique that provides quantitative phase information and high resolution over a large field-of-view. Although the technique presents numerous advantages over conventional microscopy, model mismatch due to unknown optical aberrations can significantly limit reconstruction quality. A practical way of correcting for aberrations without additional data capture is through algorithmic self-calibration, in which a pupil recovery step is embedded into the reconstruction algorithm. However, software-only aberration correction is limited in accuracy. Here, we evaluate the merits of implementing a simple, dedicated calibration procedure for applications requiring high accuracy. In simulations, we find that for a target sample reconstruction error, we can image without any aberration corrections only up to a maximum aberration magnitude of
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1039/D1LC00719J
