A locally-built, LLM-digested index of recent arXiv papers in quant finance, geometry/topology, and statistical ML — keyword search served straight from SQLite on this machine.
Multi-StyleGAN simulates live cell microscopy imagery.
DISPR uses diffusion models to predict 3D cell shapes from 2D images.
New method extracts biological concepts from cell microscopy images.
Few-shot cell segmentation from diverse sources to target domain.
A novel method detects multiple mitosis events and mitigates annotation gaps in phase-contrast microscopy.
Convolutional neural networks (CNN) have achieved state of the art performance on both classification and segmentation tasks. Applying CNNs to microscopy images is challenging due to the lack of datasets labeled at the single cell level. We extend the application of CNNs to microscopy image classification and segmentat…
We present a conditional generative model to learn variation in cell and nuclear morphology and the location of subcellular structures from microscopy images. Our model generalizes to a wide range of subcellular localization and allows for a probabilistic interpretation of cell and nuclear morphology and structure loca…
Fluorescence microscopy has enabled a dramatic development in modern biology. Due to its inherently weak signal, fluorescence microscopy is not only much noisier than photography, but also presented with Poisson-Gaussian noise where Poisson noise, or shot noise, is the dominating noise source. To get clean fluorescence…
We study the problem of instance segmentation in biological images with crowded and compact cells. We formulate this task as an integer program where variables correspond to cells and constraints enforce that cells do not overlap. To solve this integer program, we propose a column generation formulation where the prici…
Determining the localization of specific protein in human cells is important for understanding cellular functions and biological processes of underlying diseases. Among imaging techniques, high-throughput fluorescence microscopy imaging is an efficient biotechnology to stain the protein of interest in a cell. In this w…
TIMELY improves consistency in labeling blood cell images.
Counting and classifying blood cells is an important diagnostic tool in medicine. Support Vector Machines are increasingly popular and efficient and could replace artificial neural network systems. Here a method to classify blood cells is proposed using SVM. A set of statistics on images are implemented in C++. The MPE…
In this paper, we propose a novel application of Generative Adversarial Networks (GAN) to the synthesis of cells imaged by fluorescence microscopy. Compared to natural images, cells tend to have a simpler and more geometric global structure that facilitates image generation. However, the correlation between the spatial…
With super-resolution optical microscopy, it is now possible to observe molecular interactions in living cells. The obtained images have a very high spatial precision but their overall quality can vary a lot depending on the structure of interest and the imaging parameters. Moreover, evaluating this quality is often di…
Multi-domain learning (MDL) aims at obtaining a model with minimal average risk across multiple domains. Our empirical motivation is automated microscopy data, where cultured cells are imaged after being exposed to known and unknown chemical perturbations, and each dataset displays significant experimental bias. This p…
Visualizing the details of different cellular structures is of great importance to elucidate cellular functions. However, it is challenging to obtain high quality images of different structures directly due to complex cellular environments. Fluorescence staining is a popular technique to label different structures but …
Deep learning reduces artifacts in limited angle X-ray microscopy.
We propose a new deep learning approach for medical imaging that copes with the problem of a small training set, the main bottleneck of deep learning, and apply it for classification of healthy and cancer cells acquired by quantitative phase imaging. The proposed method, called transferring of pre-trained generative ad…
Understanding if classifiers generalize to out-of-sample datasets is a central problem in machine learning. Microscopy images provide a standardized way to measure the generalization capacity of image classifiers, as we can image the same classes of objects under increasingly divergent, but controlled factors of variat…
DVNet efficiently segments large neurovascular datasets using skip connections.
Super-resolution fluorescence microscopy, with a resolution beyond the diffraction limit of light, has become an indispensable tool to directly visualize biological structures in living cells at a nanometer-scale resolution. Despite advances in high-density super-resolution fluorescent techniques, existing methods stil…
Deep learning improves 3D microscopy resolution without matched target images.
Method estimates section thickness and XY anisotropy in ssEM images.
We discuss recently emerging applications of the state-of-art deep learning methods on optical microscopy and microscopic image reconstruction, which enable new transformations among different modes and modalities of microscopic imaging, driven entirely by image data. We believe that deep learning will fundamentally ch…
We introduce a novel Deep Learning framework, which quantitatively estimates image segmentation quality without the need for human inspection or labeling. We refer to this method as a Quality Assurance Network -- QANet. Specifically, given an image and a `proposed' corresponding segmentation, obtained by any method inc…
Machine learning classifies colorectal tissue using photoacoustic microscopy.
Topology-enhanced loss improves 3D object reconstruction from 2D images.
Machine learning speeds up FLIM analysis in biomedical research.
Deconvolution microscopy has been extensively used to improve the resolution of the widefield fluorescent microscopy. Conventional approaches, which usually require the point spread function (PSF) measurement or blind estimation, are however computationally expensive. Recently, CNN based approaches have been explored a…
Malaria is a life-threatening disease affecting millions. Microscopy-based assessment of thin blood films is a standard method to (i) determine malaria species and (ii) quantitate high-parasitemia infections. Full automation of malaria microscopy by machine learning (ML) is a challenging task because field-prepared sli…
Study improves pollen detection in optical and holographic images using deep learning.
We propose a general framework for denoising high-dimensional measurements which requires no prior on the signal, no estimate of the noise, and no clean training data. The only assumption is that the noise exhibits statistical independence across different dimensions of the measurement, while the true signal exhibits s…
Prototype for adaptive electron microscopy scans reduces dose and time.
UDVD uses deep learning to denoise videos without supervision.
An image dataset of 10 different size molecules, where each molecule has 2,000 structural variants, is generated from the 2D cross-sectional projection of Molecular Dynamics trajectories. The purpose of this dataset is to provide a benchmark dataset for the increasing need of machine learning, deep learning and image p…
Deep learning methods are becoming widely used for restoration of defects associated with fluorescence microscopy imaging. One of the major challenges in application of such methods is the availability of training data. In this work, we propose a unified method for reconstruction of multi-defect fluorescence microscopy…
Improves spline quality and accuracy in computational microscopy.
Unsupervised clustering of curves according to their shapes is an important problem with broad scientific applications. The existing model-based clustering techniques either rely on simple probability models (e.g., Gaussian) that are not generally valid for shape analysis or assume the number of clusters. We develop an…
Understanding the three-dimensional (3D) structure of the genome is essential for elucidating vital biological processes and their links to human disease. To determine how the genome folds within the nucleus, chromosome conformation capture methods such as HiC have recently been employed. However, computational methods…
AI enhances pollen recognition in veterinary imaging using holographic microscopy.
Cryo-electron microscopy (cryo-EM) is an emerging experimental method to characterize the structure of large biomolecular assemblies. Single particle cryo-EM records 2D images (so-called micrographs) of projections of the three-dimensional particle, which need to be processed to obtain the three-dimensional reconstruct…
The need for labour intensive pixel-wise annotation is a major limitation of many fully supervised learning methods for segmenting bioimages that can contain numerous object instances with thin separations. In this paper, we introduce a deep convolutional neural network for microscopy image segmentation. Annotation iss…
Develops statistical guarantees for image-to-image regression models.
Due to concerns about human error in crowdsourcing, it is standard practice to collect labels for the same data point from multiple internet workers. We here show that the resulting budget can be used more effectively with a flexible worker assignment strategy that asks fewer workers to analyze easy-to-label data and m…
The detection of interesting patterns in large high-dimensional datasets is difficult because of their dimensionality and pattern complexity. Therefore, analysts require automated support for the extraction of relevant patterns. In this paper, we present FDive, a visual active learning system that helps to create visua…
We investigate the use of a non-parametric independence measure, the Hilbert-Schmidt Independence Criterion (HSIC), as a loss-function for learning robust regression and classification models. This loss-function encourages learning models where the distribution of the residuals between the label and the model predictio…
New method separates objects from images using deep neural networks trained to inpaint.
Algorithm aligns 3D density maps using Wasserstein distance.