Biological imaging最新文献

Non-alcoholic fatty liver disease (NAFLD) is now the leading cause of chronic liver disease, affecting approximately 30% of people worldwide. Histopathology reading of fibrosis patterns is crucial to diagnosing NAFLD. In particular, separating mild from severe stages corresponds to a critical transition as it correlates with clinical outcomes. Deep Learning for digitized histopathology whole-slide images (WSIs) can reduce high inter- and intra-rater variability. We demonstrate a novel solution to score fibrosis severity on a retrospective cohort of 152 Sirius-Red WSIs, with fibrosis stage annotated at slide level by an expert pathologist. We exploit multiple instance learning and multiple-inferences to address the sparsity of pathological signs. We achieved an accuracy of , an F1 score of and an AUC of . These results set new state-of-the-art benchmarks for this application.

High-content screening (HCS) provides an excellent tool to understand the mechanism of action of drugs on disease-relevant model systems. Careful selection of fluorescent labels (FLs) is crucial for successful HCS assay development. HCS assays typically comprise (a) FLs containing biological information of interest, and (b) additional structural FLs enabling instance segmentation for downstream analysis. However, the limited number of available fluorescence microscopy imaging channels restricts the degree to which these FLs can be experimentally multiplexed. In this article, we present a segmentation workflow that overcomes the dependency on structural FLs for image segmentation, typically freeing two fluorescence microscopy channels for biologically relevant FLs. It consists in extracting structural information encoded within readouts that are primarily biological, by fine-tuning pre-trained state-of-the-art generalist cell segmentation models for different combinations of individual FLs, and aggregating the respective segmentation results together. Using annotated datasets that we provide, we confirm our methodology offers improvements in performance and robustness across several segmentation aggregation strategies and image acquisition methods, over different cell lines and various FLs. It thus enables the biological information content of HCS assays to be maximized without compromising the robustness and accuracy of computational single-cell profiling.

Super-resolution microscopy allowed major improvements in our capacity to describe and explain biological organization at the nanoscale. Single-molecule localization microscopy (SMLM) uses the positions of molecules to create super-resolved images, but it can also provide new insights into the organization of molecules through appropriate pointillistic analyses that fully exploit the sparse nature of SMLM data. However, the main drawback of SMLM is the lack of analytical tools easily applicable to the diverse types of data that can arise from biological samples. Typically, a cloud of detections may be a cluster of molecules or not depending on the local density of detections, but also on the size of molecules themselves, the labeling technique, the photo-physics of the fluorophore, and the imaging conditions. We aimed to set an easy-to-use clustering analysis protocol adaptable to different types of data. Here, we introduce Diinamic, which combines different density-based analyses and optional thresholding to facilitate the detection of clusters. On simulated or real SMLM data, Diinamic correctly identified clusters of different sizes and densities, being performant even in noisy datasets with multiple detections per fluorophore. It also detected subdomains ("nanodomains") in clusters with non-homogeneous distribution of detections.

Image-processing pipelines require the design of complex workflows combining many different steps that bring the raw acquired data to a final result with biological meaning. In the image-processing domain of cryo-electron microscopy single-particle analysis (cryo-EM SPA), hundreds of steps must be performed to obtain the three-dimensional structure of a biological macromolecule by integrating data spread over thousands of micrographs containing millions of copies of allegedly the same macromolecule. The execution of such complicated workflows demands a specific tool to keep track of all these steps performed. Additionally, due to the extremely low signal-to-noise ratio (SNR), the estimation of any image parameter is heavily affected by noise resulting in a significant fraction of incorrect estimates. Although low SNR and processing millions of images by hundreds of sequential steps requiring substantial computational resources are specific to cryo-EM, these characteristics may be shared by other biological imaging domains. Here, we present Scipion, a Python generic open-source workflow engine specifically adapted for image processing. Its main characteristics are: (a) interoperability, (b) smart object model, (c) gluing operations, (d) comparison operations, (e) wide set of domain-specific operations, (f) execution in streaming, (g) smooth integration in high-performance computing environments, (h) execution with and without graphical capabilities, (i) flexible visualization, (j) user authentication and private access to private data, (k) scripting capabilities, (l) high performance, (m) traceability, (n) reproducibility, (o) self-reporting, (p) reusability, (q) extensibility, (r) software updates, and (s) non-restrictive software licensing.

Microscopy is a widely used method in biological research to observe the morphology and structure of cells. Amongst the plethora of microscopy techniques, fluorescent labeling with dyes or antibodies is the most popular method for revealing specific cellular organelles. However, fluorescent labeling also introduces new challenges to cellular observation, as it increases the workload, and the process may result in nonspecific labeling. Recent advances in deep visual learning have shown that there are systematic relationships between fluorescent and bright-field images, thus facilitating image translation between the two. In this article, we propose the cross-attention conditional generative adversarial network (XAcGAN) model. It employs state-of-the-art GANs (GANs) to solve the image translation task. The model uses supervised learning and combines attention-based networks to explore spatial information during translation. In addition, we demonstrate the successful application of XAcGAN to infer the health state of translated nuclei from bright-field microscopy images. The results show that our approach achieves excellent performance both in terms of image translation and nuclei state inference.

An emergent volume electron microscopy technique called cryogenic serial plasma focused ion beam milling scanning electron microscopy (pFIB/SEM) can decipher complex biological structures by building a three-dimensional picture of biological samples at mesoscale resolution. This is achieved by collecting consecutive SEM images after successive rounds of FIB milling that expose a new surface after each milling step. Due to instrumental limitations, some image processing is necessary before 3D visualization and analysis of the data is possible. SEM images are affected by noise, drift, and charging effects, that can make precise 3D reconstruction of biological features difficult. This article presents Okapi-EM, an open-source napari plugin developed to process and analyze cryogenic serial pFIB/SEM images. Okapi-EM enables automated image registration of slices, evaluation of image quality metrics specific to pFIB-SEM imaging, and mitigation of charging artifacts. Implementation of Okapi-EM within the napari framework ensures that the tools are both user- and developer-friendly, through provision of a graphical user interface and access to Python programming.

A common task in cryo-electron microscopy data processing is to compare three-dimensional density maps of macromolecules. In this paper, we propose an algorithm for aligning three-dimensional density maps, which exploits common lines between projection images of the maps. The algorithm is fully automatic and handles rotations, reflections (handedness), and translations between the maps. In addition, the algorithm is applicable to any type of molecular symmetry without requiring any information regarding the symmetry of the maps. We evaluate our alignment algorithm on publicly available density maps, demonstrating its accuracy and efficiency. The algorithm is available at https://github.com/ShkolniskyLab/emalign.