arXiv subjects

Siqi Lu

Publications and source records attributed to Siqi Lu.

21 records · Page 2Linked to original sources

arXiv2024

ASIGN: An Anatomy-aware Spatial Imputation Graphic Network for 3D Spatial Transcriptomics

Spatial transcriptomics (ST) is an emerging technology that enables medical computer vision scientists to automatically interpret the molecular profiles underlying morphological features. Currently, however, most deep learning-based ST analyses are limited to two-dimensional (2D) sections, which can introduce diagnostic errors due to the heterogeneity of pathological tissues across 3D sections. Expanding ST to three-dimensional (3D) volumes is challenging due to the prohibitive costs; a 2D ST acquisition already costs over 50 times more than whole slide imaging (WSI), and a full 3D volume with 10 sections can be an order of magnitude more expensive. To reduce costs, scientists have attempted to predict ST data directly from WSI without performing actual ST acquisition. However, these methods typically yield unsatisfying results. To address this, we introduce a novel problem setting: 3D ST imputation using 3D WSI histology sections combined with a single 2D ST slide. To do so, we present the Anatomy-aware Spatial Imputation Graph Network (ASIGN) for more precise, yet affordable, 3D ST modeling. The ASIGN architecture extends existing 2D spatial relationships into 3D by leveraging cross-layer overlap and similarity-based expansion. Moreover, a multi-level spatial attention graph network integrates features comprehensively across different data sources. We evaluated ASIGN on three public spatial transcriptomics datasets, with experimental results demonstrating that ASIGN achieves state-of-the-art performance on both 2D and 3D scenarios. Code is available at https://github.com/hrlblab/ASIGN.

cs.CV↗

arXiv2022

Engineered Octave Frequency Comb in Integrated Chalcogenide Dual-ring Microresonators

Broadband Kerr combs with a flat comb spectral profile are expected in a number of applications, such as high-capacity optical communication. Here, we propose novel concentric dual-ring microresonators (DRMs) for advanced dispersion engineering to tailor the comb spectral profile. The dispersion can be flexibly engineered not only by the cross-section of the DRMs, but also by the gap between concentric dual-ring microresonators, which provides a new path to geometrically control the spectral profile of the soliton Kerr combs. An octave-spanning dissipative Kerr soliton comb with superior spectral flatness has been achieved numerically, covering from the telecommunication band to the mid-infrared (MIR) band region with a -40 dB bandwidth of 1265 nm (99.82 THz). Our results are promising to fully understand the nonlinear dynamics in hybrid modes in DRMs, which helps control broadband comb formation.

physics.optics↗

arXiv2020

Investigation of plasmonic evolution of atomically size-selected Au clusters by electron energy loss spectrum--from solid state to molecular scale

Versatile quantum modes emerge for plasmon describing the collective oscillations of free electrons in metallic nanoparticles when the particle sizes are greatly reduced. Rather than traditional nanoscale study, the understanding of quantum plasmon desires extremal atomic control of the nanoparticles, calling for size dependent plasmon measurement over a series of nanoparticles with atomically adjustable atom number over several orders of magnitude. Here we report the N dependent plasmonic evolution of atomically size selected gold particles with N= 100 70000 using electron energy loss (EEL) spectroscopy in a scanning transmission electron microscope. The EEL mapping assigns a feature at 2.7 eV as the bulk plasmon and another at 2.4 eV as surface plasmon, which evolution reveals three regimes. When N decreases from 70000 to 887, the bulk plasmon stays unchanged while the surface plasmon exhibits a slight red shift from 2.4 to 2.3 eV. It can be understood by the dominance of classical plasmon physics and electron boundary scattering induced retardation. When N further decreases from 887 to 300, the bulk plasmon disappears totally and the surface plasmon shows a steady blueshift, which indicates that the quantum confinement emerges and modifies the intraband transition. When N 100 300, the plasmon is split to three fine features, which is attributed to superimposed single electron transitions between the quantized molecular like energy level by the time dependent density functional theory calculations. The surface plasmon's excitation ratio has a scaling law with an exponential dependence on N ( N^0.669), essentially the square of the radius. A unified evolution picture from the classical to quantum, molecular plasmon is thus demonstrated.

physics.atm-clus↗