In the last few years, image processing researchers spent a substantial amount of time and effort developing and perfecting image quality assessment algorithms. Bright-field microscopy, for example, produces images whose quality is a bottleneck for consistent evaluation. For instance, when a stack of images of a specimen is acquired in different focal plane configurations, there will be a set of blurred or partially blurred elements in it, impairing proper evaluation. This work aims to provide an image quality assessment metric, without the presence of a reference image for comparison, to detect the blurred and sharp images among the whole set of the stack, and elect the sharpest ones for a further fusion process. The correlation of the results with subjective labeling of the image sets showed that the proposed metric offers reliable identification of the eligible images for fusion and suggests the application in other real-world problems.
Investigation of cell structure is hardly imaginable without bright-field microscopy. Numerous modifications such as depth-wise scanning or videoenhancement make this method being state-of-the-art. This raises a question what maximal information can be extracted from ordinary (but well acquired) bright-field images in a model-free way. Here we introduce a method of a physically correct extraction of features for each pixel when these features resemble a transparency spectrum. The method is compatible with existent ordinary bright-field microscopes and requires mathematically sophisticated data…
The most realistic information about the transparent sample such as a live cell can be obtained only using bright-field light microscopy. At high-intensity pulsing LED illumination, we captured a primary 12-bit-per-channel (bpc) response from an observed sample using a bright-field microscope equipped with a high-resolution (4872x3248) image sensor. In order to suppress data distortions originating from the light interactions with elements in the optical path, poor sensor reproduction (geometrical defects of the camera sensor and some peculiarities of sensor sensitivity), we propose a spectros…
Detecting and segmenting individual cells from microscopy images is critical to various life science applications. Traditional cell segmentation tools are often ill-suited for applications in brightfield microscopy due to poor contrast and intensity heterogeneity, and only a small subset are applicable to segment cells in a cluster. In this regard, we introduce a novel supervised technique for cell segmentation in a multi-task learning paradigm. A combination of a multi-task loss, based on the region and cell boundary detection, is employed for an improved prediction efficiency of the network.…
University of South Bohemia in České Budějovice（捷克布杰约维采南波希米亚大学）；Helmholtz Centre Potsdam GFZ German Research Centre for Geosciences（亥姆霍兹波茨坦中心德国地球科学研究中心）
Living cell segmentation from bright-field light microscopy images is challenging due to the image complexity and temporal changes in the living cells. Recently developed deep learning (DL)-based methods became popular in medical and microscopy image segmentation tasks due to their success and promising outcomes. The main objective of this paper is to develop a deep learning, U-Net-based method to segment the living cells of the HeLa line in bright-field transmitted light microscopy. To find the most suitable architecture for our datasets, a residual attention U-Net was proposed and compared w…
We report results on unsupervised organization of cervical cells using microscopy of Pap-smear samples in brightfield (3-channel colour) as well as high resolution quantitative phase imaging modalities. A number of morphological parameters are measured for each of the 1450 cell nuclei (from $10$ woman subjects) imaged in this study. The Principal Component Analysis (PCA) methodology applied to this data shows that the cell image clustering performance improves significantly when brightfield as well as phase information is utilized for PCA as compared to when brightfield-only information is use…
University of California, Los Angeles（加利福尼亚大学洛杉矶分校）；California NanoSystems Institute (CNSI)（加州纳米系统研究所）；David Geffen School of Medicine（大卫·格芬医学院）
Using a deep neural network, we demonstrate a digital staining technique, which we term PhaseStain, to transform quantitative phase images (QPI) of labelfree tissue sections into images that are equivalent to brightfield microscopy images of the same samples that are histochemically stained. Through pairs of image data (QPI and the corresponding brightfield images, acquired after staining) we train a generative adversarial network (GAN) and demonstrate the effectiveness of this virtual staining approach using sections of human skin, kidney and liver tissue, matching the brightfield microscopy …
Deep-learning Assisted Detection and Quantification of (oo)cysts of Giardia and Cryptosporidium on Smartphone Microscopy Images
Nepal Applied Mathematics and Informatics Institute for research (NAAMII)（尼泊尔应用数学与信息学研究所（NAAMII））；Center for Analytical Sciences, Kathmandu Institute of Applied Sciences (KIAS)（加德满都应用科学学院分析科学中心）；Central Department of Chemistry, Tribhuvan University（特里布万大学化学系）
Fourier ptychographic microscopy (FPM) is a computational approach geared towards creating high-resolution and large field-of-view images without mechanical scanning. To acquire color images of histology slides, it often requires sequential acquisitions with red, green, and blue illuminations. The color reconstructions often suffer from coherent artifacts that are not presented in regular incoherent microscopy images. As a result, it remains a challenge to employ FPM for digital pathology applications, where resolution and color accuracy are of critical importance. Here we report a deep learni…
Time-lapse fluorescence microscopy (TLFM) is an important and powerful tool in synthetic biological research. Modeling TLFM experiments based on real data may enable researchers to repeat certain experiments with minor effort. This thesis is a study towards deep learning-based modeling of TLFM experiments on the image level. The modeling of TLFM experiments, by way of the example of trapped yeast cells, is split into two tasks. The first task is to generate synthetic image data based on real image data. To approach this problem, a novel generative adversarial network, for conditionalized and u…
We demonstrate a deep learning-based offline autofocusing method, termed Deep-R, that is trained to rapidly and blindly autofocus a single-shot microscopy image of a specimen that is acquired at an arbitrary out-of-focus plane. We illustrate the efficacy of Deep-R using various tissue sections that were imaged using fluorescence and brightfield microscopy modalities and demonstrate snapshot autofocusing under different scenarios, such as a uniform axial defocus as well as a sample tilt within the field-of-view. Our results reveal that Deep-R is significantly faster when compared with standard …
Crystal defects play a large role in how materials respond to their surroundings, yet there are many uncertainties in how extended defects form, move, and interact deep beneath a material's surface. A newly developed imaging diagnostic, dark-field X-ray microscopy (DFXM) can now visualize the behavior of line defects, known as dislocations, in materials under varying conditions. DFXM images visualize dislocations by imaging the very subtle long-range distortions in the material's crystal lattice, which produce a characteristic adjoined pair of bright and dark regions. Full analysis of how thes…
Practical Guidelines for Cell Segmentation Models Under Optical Aberrations in Microscopy
The Fifth Affiliated Hospital of Wenzhou Medical University（温州医科大学附属第五医院）；Tsinghua University（清华大学）；Hangzhou Dianzi University（杭州电子科技大学）；Shandong University（山东大学）
Fourier ptychographic microscopy (FPM) can achieve quantitative phase imaging with a large space-bandwidth product by synthesizing a set of low-resolution intensity images captured under angularly varying illuminations. Determining accurate illumination angles is critical because the consistency between actual systematic parameters and those used in the recovery algorithm is essential for high-quality imaging. This paper presents a full-pose-parameter and physics-based method for calibrating illumination angles. Using a physics-based model constructed with general knowledge of the employed mic…
Going Beyond U-Net: Assessing Vision Transformers for Semantic Segmentation in Microscopy Image Analysis
Institute of Computer Science, University of Tartu（塔尔图大学计算机科学研究所）；Center for Artificial Intelligence, Technical University of Applied Sciences Würzburg-Schweinfurt（维尔茨堡-施韦因富特应用技术大学人工智能中心）；STACC
Virtual birefringence imaging and histological staining of amyloid deposits in label-free tissue using autofluorescence microscopy and deep learning
University of California, Los Angeles（加州大学洛杉矶分校）；California NanoSystems Institute (CNSI), University of California, Los Angeles（加州大学洛杉矶分校加州纳米系统研究所）；Fatih Sultan Mehmet Vakif University（法提赫·苏丹·穆罕默德·瓦克夫大学）；David Geffen School of Medicine at the University of California, Los Angeles（加州大学洛杉矶分校大卫·格芬医学院）；Hadassah Hebrew University Medical Center（哈达萨希伯来大学医学中心）；Keck School of Medicine, University of Southern California（南加州大学凯克医学院）
SegmentAnything helps microscopy images based automatic and quantitative organoid detection and analysis
National Heart and Lung Institute, Imperial College London（帝国理工学院国家心肺研究所）；King’s College London（伦敦国王学院）；Eindhoven University of Technology（埃因霍温理工大学）；Institute for Complex Molecular Systems (ICMS)（复杂分子系统研究所）；Imperial College London（帝国理工学院）
本文提出利用 SegmentAnything 分割单个类器官并计算多项形态学指标的自动化显微镜分析流程，在 iPSC 衍生 NE 类器官明场图像上验证其与人工检测测量高度一致。
Cell image analysis is crucial in Alzheimer's research to detect the presence of A$β$ protein inhibiting cell function. Deep learning speeds up the process by making only low-level data sufficient for fruitful inspection. We first found Unet is most suitable in augmented microscopy by comparing performance in multi-class semantics segmentation. We develop the augmented microscopy method to capture nuclei in a brightfield image and the transformer using Unet model to convert an input image into a sequence of topological information. The performance regarding Intersection-over-Union is consisten…
PSL University（巴黎文理研究大学）；Mines Paris（巴黎矿业学院）；Centre for Computational Biology（计算生物学中心）；Institut Curie（居里研究所）；INSERM（法国国家健康与医学研究院）；University of Montpellier（蒙彼利埃大学）；IGH（人类遗传学研究所）；CNRS（法国国家科学研究中心）
Deep learning provides us with powerful methods to perform nucleus or cell segmentation with unprecedented quality. However, these methods usually require large training sets of manually annotated images, which are tedious and expensive to generate. In this paper we propose to use In Silico Labeling (ISL) as a pretraining scheme for segmentation tasks. The strategy is to acquire label-free microscopy images (such as bright-field or phase contrast) along fluorescently labeled images (such as DAPI or CellMask). We then train a model to predict the fluorescently labeled images from the label-free…
Purdue University（普渡大学）；Lawrence Berkeley National Laboratory（劳伦斯伯克利国家实验室）；Los Alamos National Laboratory（洛斯阿拉莫斯国家实验室）；Air Force Research Laboratory（美国空军研究实验室）
Many material and biological samples in scientific imaging are characterized by non-local repeating structures. These are studied using scanning electron microscopy and electron tomography. Sparse sampling of individual pixels in a 2D image acquisition geometry, or sparse sampling of projection images with large tilt increments in a tomography experiment, can enable high speed data acquisition and minimize sample damage caused by the electron beam. In this paper, we present an algorithm for electron tomographic reconstruction and sparse image interpolation that exploits the non-local redundanc…
Virtual Gram staining of label-free bacteria using darkfield microscopy and deep learning
University of California, Los Angeles（加州大学洛杉矶分校）；California NanoSystems Institute (CNSI)（加州纳米系统研究所）；Texas A&M University（德克萨斯农工大学）；Texas A&M Engineering Experiment Station（德克萨斯农工大学工程实验站）；David Geffen School of Medicine（大卫·格芬医学院）
