Related papers: Guidelines for reporting cell types: the MIRACL st…
Although cell shape can reflect the mechanical and biochemical properties of the cell and its environment, quantification of 3D cell shapes within 3D tissues remains difficult, typically requiring digital reconstruction from a stack of 2D…
Using optical speckle scanning microscopy [1], we demonstrate that clear images of multiple cells can be obtained through biological scattering tissue, with subcellular resolution and good image quality, as long as the size of the imaging…
As machine learning models become increasingly larger, trained weakly supervised on large, possibly uncurated data sets, it becomes increasingly important to establish mechanisms for inspecting, interacting, and revising models to mitigate…
The detection of rare cell types in single-cell transcriptomics data is crucial for elucidating disease pathogenesis and tissue development dynamics. However, a critical gap that persists in current methods is their inability to provide an…
Medical report generation is a critical task in healthcare that involves the automatic creation of detailed and accurate descriptions from medical images. Traditionally, this task has been approached as a sequence generation problem,…
Modern spatial microscopy has provided developmental biology with powerful research tools. However, the recent significant technological breakthroughs have inevitably led to technical "bottlenecks" for the application of the new procedures…
Large language models applied to vast biological datasets have the potential to transform biology by uncovering disease mechanisms and accelerating drug development. However, current models are often siloed, trained separately on…
We introduce CellARC, a synthetic benchmark for abstraction and reasoning built from multicolor 1D cellular automata (CA). Each episode has five support pairs and one query serialized in 256 tokens, enabling rapid iteration with small…
The application of microscopy in biomedical research has come a long way since Antonie van Leeuwenhoek discovered unicellular organisms. Countless innovations have positioned light microscopy as a cornerstone of modern biology and a method…
Motivation: Prediction of phenotypes from high-dimensional data is a crucial task in precision biology and medicine. Many technologies employ genomic biomarkers to characterize phenotypes. However, such elements are not sufficient to…
Cellular heterogeneity is an immanent property of biological systems that covers very different aspects of life ranging from genetic diversity to cell-to-cell variability driven by stochastic molecular interactions, and noise induced cell…
Biologists study Diatoms, a fundamental algae, to assess the health of aquatic systems. Diatom specimens have traditionally been preserved on analog slides, where a single slide can contain thousands of these microscopic organisms.…
In Schiebinger et al. (2017), the authors use optimal transport of measures on empirical distributions arising from biological experiments to relate the single cell RNA sequencing profiles for induced pluripotent stem cells differentiating.…
Model biomembrane systems play a crucial role in advancing biomedical research by providing simplified yet effective platforms for exploring complex biological mechanisms. These systems span a wide range of scales, from…
Identifying concentrations of components from an observed mixture is a fundamental problem in signal processing. It has diverse applications in fields ranging from hyperspectral imaging to denoising biomedical sensors. This paper focuses on…
Modern computer systems often rely on syslog, a simple, universal protocol that records every critical event across heterogeneous infrastructure. However, healthcare's rapidly growing clinical AI stack has no equivalent. As hospitals rush…
Sickle cell disease causes erythrocytes to become sickle-shaped, affecting their movement in the bloodstream and reducing oxygen delivery. It has a high global prevalence and places a significant burden on healthcare systems, especially in…
Synthetic biology brings together concepts and techniques from engineering and biology. In this field, computer-aided design (CAD) is necessary in order to bridge the gap between computational modeling and biological data. An application…
During development, spatio-temporal patterns ranging from checkerboard to engulfing occur with precise proportions of the respective cell fates. Key developmental regulators are intracellular transcriptional interactions and intercellular…
Microglia are important cells in the brain, and their shape can tell us a lot about brain health. In this project, I test three different tools for finding the center points of microglia in 3D microscope images. The tools include ilastik,…