Cagatay Isil

Cagatay Isil, Deniz Mengu, Yifan Zhao et al.

High-resolution synthesis/projection of images over a large field-of-view (FOV) is hindered by the restricted space-bandwidth-product (SBP) of wavefront modulators. We report a deep learning-enabled diffractive display design that is based on a jointly-trained pair of an electronic encoder and a diffractive optical decoder to synthesize/project super-resolved images using low-resolution wavefront modulators. The digital encoder, composed of a trained convolutional neural network (CNN), rapidly pre-processes the high-resolution images of interest so that their spatial information is encoded into low-resolution (LR) modulation patterns, projected via a low SBP wavefront modulator. The diffractive decoder processes this LR encoded information using thin transmissive layers that are structured using deep learning to all-optically synthesize and project super-resolved images at its output FOV. Our results indicate that this diffractive image display can achieve a super-resolution factor of ~4, demonstrating a ~16-fold increase in SBP. We also experimentally validate the success of this diffractive super-resolution display using 3D-printed diffractive decoders that operate at the THz spectrum. This diffractive image decoder can be scaled to operate at visible wavelengths and inspire the design of large FOV and high-resolution displays that are compact, low-power, and computationally efficient.

Cagatay Isil, Hatice Ceylan Koydemir, Merve Eryilmaz et al.

Gram staining has been one of the most frequently used staining protocols in microbiology for over a century, utilized across various fields, including diagnostics, food safety, and environmental monitoring. Its manual procedures make it vulnerable to staining errors and artifacts due to, e.g., operator inexperience and chemical variations. Here, we introduce virtual Gram staining of label-free bacteria using a trained deep neural network that digitally transforms darkfield images of unstained bacteria into their Gram-stained equivalents matching brightfield image contrast. After a one-time training effort, the virtual Gram staining model processes an axial stack of darkfield microscopy images of label-free bacteria (never seen before) to rapidly generate Gram staining, bypassing several chemical steps involved in the conventional staining process. We demonstrated the success of the virtual Gram staining workflow on label-free bacteria samples containing Escherichia coli and Listeria innocua by quantifying the staining accuracy of the virtual Gram staining model and comparing the chromatic and morphological features of the virtually stained bacteria against their chemically stained counterparts. This virtual bacteria staining framework effectively bypasses the traditional Gram staining protocol and its challenges, including stain standardization, operator errors, and sensitivity to chemical variations.

Guangdong Ma, Che-Yung Shen, Jingxi Li et al.

Unidirectional imagers form images of input objects only in one direction, e.g., from field-of-view (FOV) A to FOV B, while blocking the image formation in the reverse direction, from FOV B to FOV A. Here, we report unidirectional imaging under spatially partially coherent light and demonstrate high-quality imaging only in the forward direction (A->B) with high power efficiency while distorting the image formation in the backward direction (B->A) along with low power efficiency. Our reciprocal design features a set of spatially engineered linear diffractive layers that are statistically optimized for partially coherent illumination with a given phase correlation length. Our analyses reveal that when illuminated by a partially coherent beam with a correlation length of ~1.5 w or larger, where w is the wavelength of light, diffractive unidirectional imagers achieve robust performance, exhibiting asymmetric imaging performance between the forward and backward directions - as desired. A partially coherent unidirectional imager designed with a smaller correlation length of less than 1.5 w still supports unidirectional image transmission, but with a reduced figure of merit. These partially coherent diffractive unidirectional imagers are compact (axially spanning less than 75 w), polarization-independent, and compatible with various types of illumination sources, making them well-suited for applications in asymmetric visual information processing and communication.

Che-Yung Shen, Yuhang Li, Cagatay Isil et al.

We introduce a wavelength-multiplexed massively parallel diffractive information storage platform composed of dielectric surfaces that are structurally optimized at the wavelength scale using deep learning to store and project thousands of distinct image patterns, each assigned to a unique wavelength. Through numerical simulations in the visible spectrum, we demonstrated that our wavelength-multiplexed diffractive system can store and project over 4,000 independent desired images/patterns within its output field-of-view, with high image quality and minimal crosstalk between spectral channels. Furthermore, in a proof-of-concept experiment, we demonstrated a two-layer diffractive design that stored six distinct patterns and projected them onto the same output field of view at six different wavelengths (500, 548, 596, 644, 692, and 740 nm). This diffractive architecture is scalable and can operate at various parts of the electromagnetic spectrum without the need for material dispersion engineering or redesigning its optimized diffractive layers. The demonstrated storage capacity, reconstruction image fidelity, and wavelength-encoded massively parallel read-out of our diffractive platform offer a compact and fast-access solution for large-scale optical information storage, image projection applications.

Xiao Wang, Yiyang Wu, Yuntian Wang et al.

Despite offering high sensitivity, a high signal-to-noise ratio, and a broad spectral range, single-pixel imaging (SPI) is limited by low measurement efficiency and long data-acquisition times. To address this, we propose a wavelength-multiplexed, spatially incoherent diffractive optical processor combined with a compact/shallow digital artificial neural network (ANN) to implement compressive SPI. Specifically, we model the bucket detection process in conventional SPI as a linear intensity transformation with spatially and spectrally varying point-spread functions. This transformation matrix is treated as a learnable parameter and jointly optimized with a shallow digital ANN composed of 2 hidden nonlinear layers. The wavelength-multiplexed diffractive processor is then configured via data-free optimization to approximate this pre-trained transformation matrix; after this optimization, the diffractive processor remains static/fixed. Upon multi-wavelength illumination and diffractive modulation, the target spatial information of the input object is spectrally encoded. A single-pixel detector captures the output spectral power at each illumination band, which is then rapidly decoded by the jointly trained digital ANN to reconstruct the input image. In addition to our numerical analyses demonstrating the feasibility of this approach, we experimentally validated its proof-of-concept using an array of light-emitting diodes (LEDs). Overall, this work demonstrates a computational imaging framework for compressive SPI that can be useful in applications such as biomedical imaging, autonomous devices, and remote sensing.

Cagatay Isil, Alexander Chen, Yuhang Li et al.

3D image display is essential for next-generation volumetric imaging; however, dense depth multiplexing for 3D image projection remains challenging because diffraction-induced cross-talk rapidly increases as the axial image planes get closer. Here, we introduce a 3D display system comprising a digital encoder and a diffractive optical decoder, which simultaneously projects different images onto multiple target axial planes with high axial resolution. By leveraging multi-layer diffractive wavefront decoding and deep learning-based end-to-end optimization, the system achieves high-fidelity depth-resolved 3D image projection in a snapshot, enabling axial plane separations on the order of a wavelength. The digital encoder leverages a Fourier encoder network to capture multi-scale spatial and frequency-domain features from input images, integrates axial position encoding, and generates a unified phase representation that simultaneously encodes all images to be axially projected in a single snapshot through a jointly-optimized diffractive decoder. We characterized the impact of diffractive decoder depth, output diffraction efficiency, spatial light modulator resolution, and axial encoding density, revealing trade-offs that govern axial separation and 3D image projection quality. We further demonstrated the capability to display volumetric images containing 28 axial slices, as well as the ability to dynamically reconfigure the axial locations of the image planes, performed on demand. Finally, we experimentally validated the presented approach, demonstrating close agreement between the measured results and the target images. These results establish the diffractive 3D display system as a compact and scalable framework for depth-resolved snapshot 3D image projection, with potential applications in holographic displays, AR/VR interfaces, and volumetric optical computing.

Jingtian Hu, Kun Liao, Niyazi Ulas Dinc et al.

Phase imaging is widely used in biomedical imaging, sensing, and material characterization, among other fields. However, direct imaging of phase objects with subwavelength resolution remains a challenge. Here, we demonstrate subwavelength imaging of phase and amplitude objects based on all-optical diffractive encoding and decoding. To resolve subwavelength features of an object, the diffractive imager uses a thin, high-index solid-immersion layer to transmit high-frequency information of the object to a spatially-optimized diffractive encoder, which converts/encodes high-frequency information of the input into low-frequency spatial modes for transmission through air. The subsequent diffractive decoder layers (in air) are jointly designed with the encoder using deep-learning-based optimization, and communicate with the encoder layer to create magnified images of input objects at its output, revealing subwavelength features that would otherwise be washed away due to diffraction limit. We demonstrate that this all-optical collaboration between a diffractive solid-immersion encoder and the following decoder layers in air can resolve subwavelength phase and amplitude features of input objects in a highly compact design. To experimentally demonstrate its proof-of-concept, we used terahertz radiation and developed a fabrication method for creating monolithic multi-layer diffractive processors. Through these monolithically fabricated diffractive encoder-decoder pairs, we demonstrated phase-to-intensity transformations and all-optically reconstructed subwavelength phase features of input objects by directly transforming them into magnified intensity features at the output. This solid-immersion-based diffractive imager, with its compact and cost-effective design, can find wide-ranging applications in bioimaging, endoscopy, sensing and materials characterization.

Michael John Fanous, Paloma Casteleiro Costa, Cagatay Isil et al.

The integration of deep learning techniques with biophotonic setups has opened new horizons in bioimaging. A compelling trend in this field involves deliberately compromising certain measurement metrics to engineer better bioimaging tools in terms of cost, speed, and form-factor, followed by compensating for the resulting defects through the utilization of deep learning models trained on a large amount of ideal, superior or alternative data. This strategic approach has found increasing popularity due to its potential to enhance various aspects of biophotonic imaging. One of the primary motivations for employing this strategy is the pursuit of higher temporal resolution or increased imaging speed, critical for capturing fine dynamic biological processes. This approach also offers the prospect of simplifying hardware requirements/complexities, thereby making advanced imaging standards more accessible in terms of cost and/or size. This article provides an in-depth review of the diverse measurement aspects that researchers intentionally impair in their biophotonic setups, including the point spread function, signal-to-noise ratio, sampling density, and pixel resolution. By deliberately compromising these metrics, researchers aim to not only recuperate them through the application of deep learning networks, but also bolster in return other crucial parameters, such as the field-of-view, depth-of-field, and space-bandwidth product. Here, we discuss various biophotonic methods that have successfully employed this strategic approach. These techniques span broad applications and showcase the versatility and effectiveness of deep learning in the context of compromised biophotonic data. Finally, by offering our perspectives on the future possibilities of this rapidly evolving concept, we hope to motivate our readers to explore novel ways of balancing hardware compromises with compensation via AI.

Cagatay Isil, Figen S. Oktem

In the phase retrieval problem, the aim is the recovery of an unknown image from intensity-only measurements such as Fourier intensity. Although there are several solution approaches, solving this problem is challenging due to its nonlinear and ill-posed nature. Recently, learning-based approaches have emerged as powerful alternatives to the analytical methods for several inverse problems. In the context of phase retrieval, a novel plug-and-play approach that exploits learning-based prior and efficient update steps has been presented at the Computational Optical Sensing and Imaging topical meeting, with demonstrated state-of-the-art performance. The key idea was to incorporate learning-based prior to the Gerchberg-Saxton type algorithms through plug-and-play regularization. In this paper, we present the mathematical development of the method including the derivation of its analytical update steps based on half-quadratic splitting and comparatively evaluate its performance through extensive simulations on a large test dataset. The results show the effectiveness of the method in terms of both image quality, computational efficiency, and robustness to initialization and noise.

Hanlong Chen, Cagatay Isil, Tianyi Gan et al.

Image projection systems must be efficient in data storage, computation and transmission while maintaining a large space-bandwidth-product (SBP) at their output. Here, we introduce a hybrid image projection system that achieves extended depth-of-field (DOF) with improved resolution, combining a convolutional neural network (CNN)-based digital encoder with an all-optical diffractive decoder. A CNN-based encoder compresses input images into compact phase representations, which are subsequently displayed by a low-resolution (LR) projector and processed by an analog diffractive decoder for all-optical image reconstruction. This optical decoder is completely passive, designed to synthesize pixel super-resolved image projections that feature an extended DOF while eliminating the need for additional power consumption for super-resolved image reconstruction. Our pixel super-resolution (PSR) image projection system demonstrates high-fidelity image synthesis over an extended DOF of ~267xW, where W is the illumination wavelength, concurrently offering up to ~16-fold SBP improvement at each lateral plane. The proof of concept of this approach is validated through an experiment conducted in the THz spectrum, and the system is scalable across different parts of the electromagnetic spectrum. This image projection architecture can reduce data storage and transmission requirements for display systems without imposing additional power constraints on the optical decoder. Beyond extended DOF PSR image projection, the underlying principles of this approach can be extended to various applications, including optical metrology and microscopy.

Yijie Zhang, Cagatay Isil, Xilin Yang et al.

Immunohistochemistry (IHC) has transformed clinical pathology by enabling the visualization of specific proteins within tissue sections. However, traditional IHC requires one tissue section per stain, exhibits section-to-section variability, and incurs high costs and laborious staining procedures. While multiplexed IHC (mIHC) techniques enable simultaneous staining with multiple antibodies on a single slide, they are more tedious to perform and are currently unavailable in routine pathology laboratories. Here, we present a deep learning-based virtual multiplexed immunostaining framework to simultaneously generate ERG and PanCK, in addition to H&E virtual staining, enabling accurate localization and interpretation of vascular invasion in thyroid cancers. This virtual mIHC technique is based on the autofluorescence microscopy images of label-free tissue sections, and its output images closely match the histochemical staining counterparts (ERG, PanCK and H&E) of the same tissue sections. Blind evaluation by board-certified pathologists demonstrated that virtual mIHC staining achieved high concordance with the histochemical staining results, accurately highlighting epithelial cells and endothelial cells. Virtual mIHC conducted on the same tissue section also allowed the identification and localization of small vessel invasion. This multiplexed virtual IHC approach can significantly improve diagnostic accuracy and efficiency in the histopathological evaluation of vascular invasion, potentially eliminating the need for traditional staining protocols and mitigating issues related to tissue loss and heterogeneity.