Video to All-in-focus Image Reconstruction Algorithm for Automated Microscopic Urinalysis
Authors: Chinmay Nema, Hari Om Aggrawal, Dipam Goswami, Rajiv Gupta, Vinti Agarwal
Abstract
Microscopic urinalysis is a routine diagnostic test at hospitals. Recent studies have demonstrated the effectiveness of deep learning methods to automate microscopic urinalysis. These methods rely on high-quality images of the urine samples in which each cell is clearly identifiable. However, in practice, the urine sample on a glass slide has a multi-layer structure; hence, all the cells are not clearly visible within the depth of field of a lens focused at a particular focal plane. It demands acquiring multiple images at different focal planes to correctly identify each cell in a given urine sample, which is a time-consuming task. In this paper, we propose to simplify the task by recording a video, in place of acquiring multiple images, while gradually changing the focus of the lens manually by hand. A typical length of the video is from 2 to 14 seconds. We reconstruct an all-in-focus image from the recorded video frames and apply a deep learning model to detect and classify urine sediments. As a proof of concept, we conduct experiments on 14 videos acquired by a trained lab technician in a usual diagnostic lab environment and show the effectiveness of the proposed automated urinalysis pipeline with our novel reconstruction algorithm.
Extended depth of field microscopy encodes axial information into a single acquisition through engineered point spread functions, but conventional and deep optics approaches are subject to degradation in scattering tissue. We introduce DeepFilters, a scattering-aware deep optics framework that jointly optimizes a parameterized pupil filter and a digital-filter-based reconstruction network through a calibrated differentiable forward model to achieve broad generalization without retraining. Incorporating empirical scattering kernels, physics-guided regularization, and a hybrid genetic-gradient initialization strategy, DeepFilters extends the PSF from 16 micron to >400 micron in clear media and enables signal recovery beyond 120 micron deep in biological tissues, validated across fixed brain slices and sea urchin embryos.
Conventional push-broom hyperspectral imaging suffers from slow acquisition speeds, precluding real-time object detection; in contrast, snapshot spectral imaging enables instantaneous hyperspectral images (HSIs) capture, making real-time object detection feasible, yet its potential is often compromised by time-consuming post-capture reconstruction. To address this issue, we propose the Focal U-shaped Network (FUN), a novel end-to-end framework that jointly performs HSI reconstruction and object detection via multi-task learning. FUN employs a shared U-shaped backbone, where reconstruction provides underlying spectral information while detection guides semantic-aware priors learning, facilitating mutually beneficial task interaction. Crucially, we introduce focal modulation, an efficient alternative to self-attention that modulates spatial and spectral features while reducing quadratic computational complexity, enabling a self-attention-free architecture for joint reconstruction and detection. Furthermore, we contribute a new HSI object detection dataset with 8712 annotated objects across 363 HSIs to facilitate evaluation of the proposed method. Experiments demonstrate that FUN achieves state-of-the-art performance on both tasks, using 40% fewer parameters and 30% less computation than recent alternatives, making it promising for future real-time edge deployment. The code and datasets are available: https://github.com/ShawnDong98/FUN.
Microscopic image analysis has long been recognized as a promising approach for monitoring activated sludge. In recent years, deep learning-based image analysis has been increasingly adopted in this field because of its high performance. However, previous studies on microscopic image analysis of activated sludge have rarely explored transformer-based models or self-supervised foundation models and have instead relied on CNNs and supervised ImageNet pretraining. In addition, previous studies often downsampled image sizes, but the effects of downsampling have not been sufficiently investigated, and the relationship between downsampling strategies and image analysis performance remains unclear. Furthermore, no study has quantitatively compared deep learning performance with quantitative image analysis (QIA), which was widely used before the emergence of deep learning. In this study, to examine how model architecture and learning strategies affect performance in microscopic image analysis of activated sludge and to quantitatively determine whether deep learning outperforms QIA, we prepared three types of activated sludge samples, classified their microscopic images, and evaluated classification accuracy. Our results showed that transformer-based architectures and alternative pretraining methods were effective in terms of classification accuracy. Our downsampling analysis showed that using overly small images reduced accuracy, but increasing image size beyond a certain point did not improve it further. In addition, the analysis indicated that, to achieve high classification accuracy, maintaining the field of view was a more effective downsampling strategy than maintaining resolution. Finally, our comparison between deep learning and QIA showed that deep learning outperformed QIA in terms of accuracy.