Automated HER2 Scoring in Breast Cancer Images Using Deep Learning and Pyramid Sampling

Human epidermal growth factor receptor 2 (HER2) is a critical protein in cancer cell growth that signifies the aggressiveness of breast cancer (BC) and helps predict its prognosis. Accurate assessment of immunohistochemically (IHC) stained tissue slides for HER2 expression levels is essential for both treatment guidance and understanding of cancer mechanisms. Nevertheless, the traditional workflow of manual examination by board-certified pathologists encounters challenges, including inter- and intra-observer inconsistency and extended turnaround times. Here, we introduce a deep learning-based approach utilizing pyramid sampling for the automated classification of HER2 status in IHC-stained BC tissue images. Our approach analyzes morphological features at various spatial scales, efficiently managing the computational load and facilitating a detailed examination of cellular and larger-scale tissue-level details. This method addresses the tissue heterogeneity of HER2 expression by providing a comprehensive view, leading to a blind testing classification accuracy of 84.70%, on a dataset of 523 core images from tissue microarrays. Our automated system, proving reliable as an adjunct pathology tool, has the potential to enhance diagnostic precision and evaluation speed, and might significantly impact cancer treatment planning.

Neural Network-Based Processing and Reconstruction of Compromised Biophotonic Image Data

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.

Multiplane Quantitative Phase Imaging Using a Wavelength-Multiplexed Diffractive Optical Processor

Quantitative phase imaging (QPI) is a label-free technique that provides optical path length information for transparent specimens, finding utility in biology, materials science, and engineering. Here, we present quantitative phase imaging of a 3D stack of phase-only objects using a wavelength-multiplexed diffractive optical processor. Utilizing multiple spatially engineered diffractive layers trained through deep learning, this diffractive processor can transform the phase distributions of multiple 2D objects at various axial positions into intensity patterns, each encoded at a unique wavelength channel. These wavelength-multiplexed patterns are projected onto a single field-of-view (FOV) at the output plane of the diffractive processor, enabling the capture of quantitative phase distributions of input objects located at different axial planes using an intensity-only image sensor. Based on numerical simulations, we show that our diffractive processor could simultaneously achieve all-optical quantitative phase imaging across several distinct axial planes at the input by scanning the illumination wavelength. A proof-of-concept experiment with a 3D-fabricated diffractive processor further validated our approach, showcasing successful imaging of two distinct phase objects at different axial positions by scanning the illumination wavelength in the terahertz spectrum. Diffractive network-based multiplane QPI designs can open up new avenues for compact on-chip phase imaging and sensing devices.

Virtual birefringence imaging and histological staining of amyloid deposits in label-free tissue using autofluorescence microscopy and deep learning

Systemic amyloidosis is a group of diseases characterized by the deposition of misfolded proteins in various organs and tissues, leading to progressive organ dysfunction and failure. Congo red stain is the gold standard chemical stain for the visualization of amyloid deposits in tissue sections, as it forms complexes with the misfolded proteins and shows a birefringence pattern under polarized light microscopy. However, Congo red staining is tedious and costly to perform, and prone to false diagnoses due to variations in the amount of amyloid, staining quality and expert interpretation through manual examination of tissue under a polarization microscope. Here, we report the first demonstration of virtual birefringence imaging and virtual Congo red staining of label-free human tissue to show that a single trained neural network can rapidly transform autofluorescence images of label-free tissue sections into brightfield and polarized light microscopy equivalent images, matching the histochemically stained versions of the same samples. We demonstrate the efficacy of our method with blind testing and pathologist evaluations on cardiac tissue where the virtually stained images agreed well with the histochemically stained ground truth images. Our virtually stained polarization and brightfield images highlight amyloid birefringence patterns in a consistent, reproducible manner while mitigating diagnostic challenges due to variations in the quality of chemical staining and manual imaging processes as part of the clinical workflow.

Multiplexed all-optical permutation operations using a reconfigurable diffractive optical network

Large-scale and high-dimensional permutation operations are important for various applications in e.g., telecommunications and encryption. Here, we demonstrate the use of all-optical diffractive computing to execute a set of high-dimensional permutation operations between an input and output field-of-view through layer rotations in a diffractive optical network. In this reconfigurable multiplexed material designed by deep learning, every diffractive layer has four orientations: 0, 90, 180, and 270 degrees. Each unique combination of these rotatable layers represents a distinct rotation state of the diffractive design tailored for a specific permutation operation. Therefore, a K-layer rotatable diffractive material is capable of all-optically performing up to 4^K independent permutation operations. The original input information can be decrypted by applying the specific inverse permutation matrix to output patterns, while applying other inverse operations will lead to loss of information. We demonstrated the feasibility of this reconfigurable multiplexed diffractive design by approximating 256 randomly selected permutation matrices using K=4 rotatable diffractive layers. We also experimentally validated this reconfigurable diffractive network using terahertz radiation and 3D-printed diffractive layers, providing a decent match to our numerical results. The presented rotation-multiplexed diffractive processor design is particularly useful due to its mechanical reconfigurability, offering multifunctional representation through a single fabrication process.

All-optical complex field imaging using diffractive processors

Complex field imaging, which captures both the amplitude and phase information of input optical fields or objects, can offer rich structural insights into samples, such as their absorption and refractive index distributions. However, conventional image sensors are intensity-based and inherently lack the capability to directly measure the phase distribution of a field. This limitation can be overcome using interferometric or holographic methods, often supplemented by iterative phase retrieval algorithms, leading to a considerable increase in hardware complexity and computational demand. Here, we present a complex field imager design that enables snapshot imaging of both the amplitude and quantitative phase information of input fields using an intensity-based sensor array without any digital processing. Our design utilizes successive deep learning-optimized diffractive surfaces that are structured to collectively modulate the input complex field, forming two independent imaging channels that perform amplitude-to-amplitude and phase-to-intensity transformations between the input and output planes within a compact optical design, axially spanning ~100 wavelengths. The intensity distributions of the output fields at these two channels on the sensor plane directly correspond to the amplitude and quantitative phase profiles of the input complex field, eliminating the need for any digital image reconstruction algorithms. We experimentally validated the efficacy of our complex field diffractive imager designs through 3D-printed prototypes operating at the terahertz spectrum, with the output amplitude and phase channel images closely aligning with our numerical simulations. We envision that this complex field imager will have various applications in security, biomedical imaging, sensing and material science, among others.

Subwavelength Imaging using a Solid-Immersion Diffractive Optical Processor

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.

Information hiding cameras: optical concealment of object information into ordinary images

Data protection methods like cryptography, despite being effective, inadvertently signal the presence of secret communication, thereby drawing undue attention. Here, we introduce an optical information hiding camera integrated with an electronic decoder, optimized jointly through deep learning. This information hiding-decoding system employs a diffractive optical processor as its front-end, which transforms and hides input images in the form of ordinary-looking patterns that deceive/mislead human observers. This information hiding transformation is valid for infinitely many combinations of secret messages, all of which are transformed into ordinary-looking output patterns, achieved all-optically through passive light-matter interactions within the optical processor. By processing these ordinary-looking output images, a jointly-trained electronic decoder neural network accurately reconstructs the original information hidden within the deceptive output pattern. We numerically demonstrated our approach by designing an information hiding diffractive camera along with a jointly-optimized convolutional decoder neural network. The efficacy of this system was demonstrated under various lighting conditions and noise levels, showing its robustness. We further extended this information hiding camera to multi-spectral operation, allowing the concealment and decoding of multiple images at different wavelengths, all performed simultaneously in a single feed-forward operation. The feasibility of our framework was also demonstrated experimentally using THz radiation. This optical encoder-electronic decoder-based co-design provides a novel information hiding camera interface that is both high-speed and energy-efficient, offering an intriguing solution for visual information security.

All-Optical Phase Conjugation Using Diffractive Wavefront Processing

Optical phase conjugation (OPC) is a nonlinear technique used for counteracting wavefront distortions, with various applications ranging from imaging to beam focusing. Here, we present the design of a diffractive wavefront processor to approximate all-optical phase conjugation operation for input fields with phase aberrations. Leveraging deep learning, a set of passive diffractive layers was optimized to all-optically process an arbitrary phase-aberrated coherent field from an input aperture, producing an output field with a phase distribution that is the conjugate of the input wave. We experimentally validated the efficacy of this wavefront processor by 3D fabricating diffractive layers trained using deep learning and performing OPC on phase distortions never seen by the diffractive processor during its training. Employing terahertz radiation, our physical diffractive processor successfully performed the OPC task through a shallow spatially-engineered volume that axially spans tens of wavelengths. In addition to this transmissive OPC configuration, we also created a diffractive phase-conjugate mirror by combining deep learning-optimized diffractive layers with a standard mirror. Given its compact, passive and scalable nature, our diffractive wavefront processor can be used for diverse OPC-related applications, e.g., turbidity suppression and aberration correction, and is also adaptable to different parts of the electromagnetic spectrum, especially those where cost-effective wavefront engineering solutions do not exist.

Complex-valued universal linear transformations and image encryption using spatially incoherent diffractive networks

As an optical processor, a Diffractive Deep Neural Network (D2NN) utilizes engineered diffractive surfaces designed through machine learning to perform all-optical information processing, completing its tasks at the speed of light propagation through thin optical layers. With sufficient degrees-of-freedom, D2NNs can perform arbitrary complex-valued linear transformations using spatially coherent light. Similarly, D2NNs can also perform arbitrary linear intensity transformations with spatially incoherent illumination; however, under spatially incoherent light, these transformations are non-negative, acting on diffraction-limited optical intensity patterns at the input field-of-view (FOV). Here, we expand the use of spatially incoherent D2NNs to complex-valued information processing for executing arbitrary complex-valued linear transformations using spatially incoherent light. Through simulations, we show that as the number of optimized diffractive features increases beyond a threshold dictated by the multiplication of the input and output space-bandwidth products, a spatially incoherent diffractive visual processor can approximate any complex-valued linear transformation and be used for all-optical image encryption using incoherent illumination. The findings are important for the all-optical processing of information under natural light using various forms of diffractive surface-based optical processors.