Biological Microscopy Image Analysis
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Agentic-J: An AI Agent for Biological Microscopy Image Analysis
arXiv:2606.02080v1 Announce Type: new Abstract: Biological image analysis increasingly demands integration across heterogeneous tools, programming environments, and domain knowledge that few researchers can command simultaneously. We present Agentic-J, a containerised, multi-agent AI assistant, primarily for ImageJ/Fiji that enables biologists to specify analysis tasks in natural language, from nuclei segmentation and cell tracking to multi-condition quantification. The agent generates...
Correlative X-ray imaging and fluorescence microscopy
Imaging the structural organization inside cells in their native state is essential for understanding how the arrangement and interactions among molecular components give rise to biological function. Fluorescence microscopy is one of the pivotal techniques that provides molecular specificity for imaging in real space, however, the technique is limited to labeled components. X-rays, on the contrary, are sensitive to electron density contrast and therefore to label-free samples, and probe...
Topology-aware reconstruction of cellular state landscapes from microscopy using self-supervised learning
Morphology and spatial organisation provide complementary readouts of cellular state. However, reconstructing continuous cellular state landscapes from imaging data remains challenging, particularly in dense biological cultures. Here we present SI-SimCLR, a spatially informed self-supervised learning framework that learns biologically informative representations directly from fluorescence microscopy images without requiring segmentation or manual annotation.
A Crossed Laser Phase Plate for CryoEM
The laser phase plate (LPP) enables phase-contrast imaging in cryogenic electron microscopy (cryoEM), enhancing image contrast without compromising high-resolution information. Here we report the implementation of a crossed laser phase plate (xLPP) comprising two optical cavities oriented orthogonally, installed in a ThermoFisher Scientific Krios G4 microscope equipped with a newly designed transfer lens module. We demonstrate the expected, strong contrast enhancement and stable, additive...
Thousandfold Expansion Microscopy
Biological macromolecules, such as proteins, are made of concatenated building blocks. We hypothesized that individual protein residues could be imaged by anchoring their side chains to a swellable polymer, cleaving backbone amide bonds, and expanding residues away from each other to a degree that enables them to be visualized separately. We introduce thousandfold expansion microscopy (1000ExM), a four-network interpenetrating hydrogel architecture that enables successive expansion from...
Diverse binding poses of agonistic neurotoxins on human Na<sub>v</sub>1.6
Abstract Voltage-gated sodium (Nav) channels are key targets of various venomous toxins. Deciphering the binding poses and mechanisms of action of representative toxins will help to dissect the functional mechanism of the channels and facilitate therapeutic development targeting Nav channels1,2. Here we present cryo-electron microscopy (cryo-EM) structures of distinct binding poses of three agonistic peptide toxins on the human Nav1.6–β1 channel complex.
A thalamus–brainstem attractor network drives history-biased decisions
Abstract Natural environments often change gradually, making it adaptive to bias decisions on the basis of the recent past — a phenomenon known as serial dependence1,2,3. Large-scale recordings during behaviour have identified that serial dependence is a common motif for decision-making, with neural representations of past experiences found throughout the brain4,5,6,7,8,9,10,11. However, it remains unclear whether this bias arises from dedicated neural circuits with history-specific...
Morphology-robust quantification of subcellular organization in complex cells
Quantitative analysis of subcellular protein organization is often confounded by variation in cell morphology, limiting the identification and interpretation of localization patterns in fluorescence microscopy data from morphologically complex cells, such as neurons and glia. We introduce CellAligner, an unsupervised framework that uses fused unbalanced Gromov-Wasserstein couplings to map protein distributions from morphologically distinct cells into shared anchor-cell geometries, enabling...
Instant Prior-Free Resolution Enhancement for Cross-Modality Microscopy
The resolving power of optical microscopy is fundamentally constrained by the diffraction of light, limiting our ability to visualize subcellular structures. Computational methods, particularly deconvolution, can restore blurred images but critically depend on an accurate point spread function (PSF), whose estimation is often impractical and error-prone, leading to artifacts. Here, we introduce Nonlinear Fourier Re-weighting (NFR), a rapid algorithm that operates without any prior knowledge...
New 3D microscope technology captures high-resolution tissue images at a fraction of the cost
New 3D microscope technology captures high-resolution tissue images at a fraction of the cost Sadie Harley Scientific Editor Robert Egan Associate Editor A team led by Raju Tomer, professor of biological sciences at Columbia University, has created a new design for microscopes and microscope lenses that could push 3D tissue imaging beyond state-of-the-art systems while drastically cutting costs and complexity. Details of the design were published in the journal Nature Biotechnology. Modern...