AIMC Topic: Microscopy, Fluorescence
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CellSeg3D, Self-supervised 3D cell segmentation for fluorescence microscopy.
eLife
Jun 24, 2025
Understanding the complex three-dimensional structure of cells is crucial across many disciplines in biology and especially in neuroscience. Here, we introduce a set of models including a 3D transformer (SwinUNetR) and a novel 3D self-supervised lear...
An AI-assisted fluorescence microscopic system for screening mitophagy inducers by simultaneous analysis of mitophagic intermediates.
Nature communications
Jun 4, 2025
Mitophagy, the selective autophagic elimination of mitochondria, is essential for maintaining mitochondrial quality and cell homeostasis. Impairment of mitophagy flux, a process involving multiple sequential intermediates, is implicated in the onset ...
Pixel super-resolved virtual staining of label-free tissue using diffusion models.
Nature communications
May 30, 2025
Virtual staining of tissue offers a powerful tool for transforming label-free microscopy images of unstained tissue into equivalents of histochemically stained samples. This study presents a diffusion model-based pixel super-resolution virtual staini...
A Benchmark for Virus Infection Reporter Virtual Staining in Fluorescence and Brightfield Microscopy.
Scientific data
May 28, 2025
Detecting virus-infected cells in light microscopy requires a reporter signal commonly achieved by immunohistochemistry or genetic engineering. While classification-based machine learning approaches to the detection of virus-infected cells have been ...
A new dataset for measuring the performance of blood vessel segmentation methods under distribution shifts.
PloS one
May 27, 2025
Creating a dataset for training supervised machine learning algorithms can be a demanding task. This is especially true for blood vessel segmentation since one or more specialists are usually required for image annotation, and creating ground truth l...
Extensible Immunofluorescence (ExIF) accessibly generates high-plexity datasets by integrating standard 4-plex imaging data.
Nature communications
May 17, 2025
Standard immunofluorescence imaging captures just ~4 molecular markers (4-plex) per cell, limiting dissection of complex biology. Inspired by multimodal omics-based data integration approaches, we propose an Extensible Immunofluorescence (ExIF) frame...
Evaluating safe infrared neural stimulation parameters: Calcium dynamics and excitotoxicity thresholds in dorsal root ganglia neurons.
Journal of neuroscience methods
May 16, 2025
BACKGROUND: As a promising neural stimulation technique, infrared neural stimulation (INS) has recently gained significant attention due to its ability to stimulate neuronal activities without needing exogenous agents. NIR light is absorbed by water ...
MLDA-Net: Multi-Level Deep Aggregation Network for 3D Nuclei Instance Segmentation.
IEEE journal of biomedical and health informatics
May 6, 2025
Segmentation of cell nuclei from three-dimensional (3D) volumetric fluorescence microscopy images is crucial for biological and clinical analyses. In recent years, convolutional neural networks have become the reliable 3D medical image segmentation s...
Single Molecule Localization Super-resolution Dataset for Deep Learning with Paired Low-resolution Images.
Scientific data
Apr 23, 2025
Deep learning super-resolution microscopy has advanced rapidly in recent years. Super-resolution images acquired by single molecule localization microscopy (SMLM) are ideal sources for high-quality datasets. However, the scarcity of public datasets l...
Predicting cell cycle stage from 3D single-cell nuclear-stained images.
Life science alliance
Apr 3, 2025
The cell cycle governs the proliferation of all eukaryotic cells. Profiling cell cycle dynamics is therefore central to basic and biomedical research. However, current approaches to cell cycle profiling involve complex interventions that may confound...
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