Related papers: Reproducible image-based profiling with Pycytomine…
For over two decades, image-based profiling has revolutionized cell phenotype analysis. Image-based profiling processes rich, high-throughput, microscopy data into thousands of unbiased measurements that reveal phenotypic patterns powerful…
Biological image analysis has traditionally focused on measuring specific visual properties of interest for cells or other entities. A complementary paradigm gaining increasing traction is image-based profiling - quantifying many distinct…
Bright-field microscopy, a cost-effective solution for live-cell culture, is often the only resource available, along with standard CPUs, for many low-budget labs. The inherent challenges of bright-field images -- their noisiness, low…
There is a need for open-source libraries in emission tomography that (i) use modern and popular backend code to encourage community contributions and (ii) offer support for the multitude of reconstruction techniques available in recent…
BioImageLoader (BIL) is a python library that handles bioimage datasets for machine learning applications, easing simple workflows and enabling complex ones. BIL attempts to wrap the numerous and varied bioimages datasets in unified…
Summary: Medical researchers obtain knowledge about the prevention and treatment of disability and disease using physical measurements and image data. To assist in this endeavor, feature extraction packages are available that are designed…
While deep learning has seen many recent applications to drug discovery, most have focused on predicting activity or toxicity directly from chemical structure. Phenotypic changes exhibited in cellular images are also indications of the…
X-ray ptychography provides exceptional nanoscale resolution and is widely applied in materials science, biology, and nanotechnology. However, its full potential is constrained by the critical challenge of accurately reconstructing images…
Background and Objective: Deep learning enables tremendous progress in medical image analysis. One driving force of this progress are open-source frameworks like TensorFlow and PyTorch. However, these frameworks rarely address issues…
Whole Slide Image (WSI) analysis plays a crucial role in modern digital pathology, enabling large-scale feature extraction from tissue samples. However, traditional feature extraction pipelines based on tools like CellProfiler often involve…
The open-source PyNX toolkit [Favre-Nicolin et al (2011) arXiv:1010.2641, Mandula et al (2016)] has been extended to provide tools for coherent X-ray imaging data analysis and simulation. All calculations can be executed on graphical…
Motivation: In recent years, image-based biological assays have steadily become high-throughput, sparking a need for fast automated methods to extract biologically-meaningful information from hundreds of thousands of images. Taking…
Portable backscatter imaging systems (PBI) integrate an X-ray source and detector in a single unit, utilizing Compton scattering photons to rapidly acquire superficial or shallow structural information of an inspected object through…
CellProfiler is a widely used software for creating reproducible, reusable image analysis workflows without needing to code. In addition to the >90 modules that make up the main CellProfiler program, CellProfiler has a plugins system that…
The pose-guided person image generation task requires synthesizing photorealistic images of humans in arbitrary poses. The existing approaches use generative adversarial networks that do not necessarily maintain realistic textures or need…
Computational pathology has made significant progress in recent years, fueling advances in both fundamental disease understanding and clinically ready tools. This evolution is driven by the availability of large amounts of digitized slides…
Visual microscopic study of diseased tissue by pathologists has been the cornerstone for cancer diagnosis and prognostication for more than a century. Recently, deep learning methods have made significant advances in the analysis and…
Major advancements in fields as diverse as biology and quantum computing have relied on a multitude of microscopic techniques. All optical, electron and scanning probe microscopy advanced with new detector technologies and integration of…
X-ray Ptychography is an advanced computational microscopy technique which is delivering exceptionally detailed quantitative imaging of biological and nanotechnology specimens. However coarse parametrisation in propagation distance,…
The integration of artificial intelligence (AI) into pathology is advancing precision medicine by improving diagnosis, treatment planning, and patient outcomes. Digitised whole-slide images (WSIs) capture rich spatial and morphological…