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Jan 6

Imaging and controlling electron motion and chemical structural dynamics of biological system in real time and space

Ultrafast electron microscopy (UEM) has found widespread applications in physics, chemistry, and materials science, enabling real-space imaging of dynamics on ultrafast timescales. Recent advances have pushed the temporal resolution of UEM into the attosecond regime, enabling the attomicroscopy technique to directly visualize electron motion. In this work, we extend the capabilities of this powerful imaging tool to investigate ultrafast electron dynamics in a biological system by imaging and controlling light induced electronic and chemical changes in the conductive network of multicellular cable bacteria. Using electron energy loss spectroscopy (EELS), we first observed a laser induced increase in {\pi}-electron density, accompanied by spectral peak broadening and a blueshift features indicative of enhanced conductivity and structural modification. We also traced the effect of ultrafast laser pumping on bulk plasmon electron oscillations by monitoring changes in the plasmon like resonance peak. Additionally, we visualized laser induced chemical structural changes in cable bacteria in real space. The imaging results revealed carbon enrichment alongside a depletion of nitrogen and oxygen, highlighting the controllability of chemical dynamics. Moreover, time resolved EELS measurements further revealed a picosecond scale decay and recovery of both {\pi}-electron and plasmonic features, attributed to electron phonon coupling. In addition to shedding light on the mechanism of electron motion in cable bacteria, these findings demonstrate ultrafast modulation and switching of conductivity, underscoring their potential as bio-optoelectronic components operating on ultrafast timescales.

  • 7 authors
·
Oct 2, 2025

ATOMMIC: An Advanced Toolbox for Multitask Medical Imaging Consistency to facilitate Artificial Intelligence applications from acquisition to analysis in Magnetic Resonance Imaging

AI is revolutionizing MRI along the acquisition and processing chain. Advanced AI frameworks have been developed to apply AI in various successive tasks, such as image reconstruction, quantitative parameter map estimation, and image segmentation. Existing frameworks are often designed to perform tasks independently or are focused on specific models or datasets, limiting generalization. We introduce ATOMMIC, an open-source toolbox that streamlines AI applications for accelerated MRI reconstruction and analysis. ATOMMIC implements several tasks using DL networks and enables MultiTask Learning (MTL) to perform related tasks integrated, targeting generalization in the MRI domain. We first review the current state of AI frameworks for MRI through a comprehensive literature search and by parsing 12,479 GitHub repositories. We benchmark 25 DL models on eight publicly available datasets to present distinct applications of ATOMMIC on accelerated MRI reconstruction, image segmentation, quantitative parameter map estimation, and joint accelerated MRI reconstruction and image segmentation utilizing MTL. Our findings demonstrate that ATOMMIC is the only MTL framework with harmonized complex-valued and real-valued data support. Evaluations on single tasks show that physics-based models, which enforce data consistency by leveraging the physical properties of MRI, outperform other models in reconstructing highly accelerated acquisitions. Physics-based models that produce high reconstruction quality can accurately estimate quantitative parameter maps. When high-performing reconstruction models are combined with robust segmentation networks utilizing MTL, performance is improved in both tasks. ATOMMIC facilitates MRI reconstruction and analysis by standardizing workflows, enhancing data interoperability, integrating unique features like MTL, and effectively benchmarking DL models.

  • 4 authors
·
Apr 30, 2024