arXiv subjects

Rachel Glenn

Publications and source records attributed to Rachel Glenn.

5 recordsLinked to original sources

arXiv2025

Two Stage Segmentation of Cervical Tumors using PocketNet

Cervical cancer remains the fourth most common malignancy amongst women worldwide.1 Concurrent chemoradiotherapy (CRT) serves as the mainstay definitive treatment regimen for locally advanced cervical cancers and includes external beam radiation followed by brachytherapy.2 Integral to radiotherapy treatment planning is the routine contouring of both the target tumor at the level of the cervix, associated gynecologic anatomy and the adjacent organs at risk (OARs). However, manual contouring of these structures is both time and labor intensive and associated with known interobserver variability that can impact treatment outcomes. While multiple tools have been developed to automatically segment OARs and the high-risk clinical tumor volume (HR-CTV) using computed tomography (CT) images,3,4,5,6 the development of deep learning-based tumor segmentation tools using routine T2-weighted (T2w) magnetic resonance imaging (MRI) addresses an unmet clinical need to improve the routine contouring of both anatomical structures and cervical cancers, thereby increasing quality and consistency of radiotherapy planning. This work applied a novel deep-learning model (PocketNet) to segment the cervix, vagina, uterus, and tumor(s) on T2w MRI. The performance of the PocketNet architecture was evaluated, when trained on data via five-fold cross validation. PocketNet achieved a mean Dice-Sorensen similarity coefficient (DSC) exceeding 70% for tumor segmentation and 80% for organ segmentation. Validation on a publicly available dataset from The Cancer Imaging Archive (TCIA) demonstrated the models robustness, achieving DSC scores of 67.3% for tumor segmentation and 80.8% for organ segmentation. These results suggest that PocketNet is robust to variations in contrast protocols, providing reliable segmentation of the regions of interest.

cs.CV↗

arXiv2024

MIST: A Simple and Scalable End-To-End 3D Medical Imaging Segmentation Framework

Medical imaging segmentation is a highly active area of research, with deep learning-based methods achieving state-of-the-art results in several benchmarks. However, the lack of standardized tools for training, testing, and evaluating new methods makes the comparison of methods difficult. To address this, we introduce the Medical Imaging Segmentation Toolkit (MIST), a simple, modular, and end-to-end medical imaging segmentation framework designed to facilitate consistent training, testing, and evaluation of deep learning-based medical imaging segmentation methods. MIST standardizes data analysis, preprocessing, and evaluation pipelines, accommodating multiple architectures and loss functions. This standardization ensures reproducible and fair comparisons across different methods. We detail MIST's data format requirements, pipelines, and auxiliary features and demonstrate its efficacy using the BraTS Adult Glioma Post-Treatment Challenge dataset. Our results highlight MIST's ability to produce accurate segmentation masks and its scalability across multiple GPUs, showcasing its potential as a powerful tool for future medical imaging research and development.

eess.IV↗

arXiv2019

Conceptual Insights into the Interaction of the Phase of the Electric Field and Molecular Spectroscopy to Further Understand Molecular Isomerization and Solute-Solvent Interactions

The real and imaginary parts of the susceptibility are fundamentally associated with the molecular dispersion and absorption, respectively. Measurement of the molecular dispersion has given insight into underlying molecular dynamics such as the identification of conical intersections and solute-solvent interactions. We show that when using a shaped pulse(s), it is possible to mix the real and imaginary parts of the nonlinear susceptibility into the molecular absorption. We then explain how to separate the real and imaginary parts of the nonlinear susceptibility when using a shaped pulse(s). We describe how the imaginary (absorption-like) and real (dispersion-like) parts of the nonlinear susceptibility can be used to understand molecular dynamics involving conical intersections in solvated molecules. We calculate the inhomogenous lineshape for a solvated molecule and show that when the phase is resonant with a vibrational line that the lineshape changes from absorption-like to dispersion-like. We find that the linear polarization is sensitive to the phase of the pulse.

physics.chem-ph↗

arXiv2014

Multidimensional spectroscopy with a single broadband phase-shaped laser pulse

We calculate the frequency-dispersed nonlinear transmission signal of a phase-shaped visible pulse to fourth order in the field. Two phase profiles, a phase-step and phase-pulse, are considered. Two dimensional signals obtained by varying the detected frequency and phase parameters are presented for a three electronic band model system. We demonstrate how two-photon and stimulated Raman resonances can be manipulated by the phase profile and sign, and selected quantum pathways can be suppressed.

physics.chem-ph↗

arXiv2014

Nonlinear transmission spectroscopy with dual frequency combs

We show how two frequency combs $\mathcal{E}_1$, $\mathcal{E}_2$ can be used to measure single-photon, two-photon absorption (TPA), and Raman resonances in a molecule with three electronic bands, by detecting the radio frequency modulation of the nonlinear transmission signal. Some peaks are independent of the carrier frequency of the comb and others shift with that frequency and have a width close to the comb width. TPA and Raman resonances independent of the carrier frequency are selected by measuring the transmission signal $\sim\mathcal{E}_1^2 \mathcal{E}_2^2$ and the single-photon resonances are selected by measuring the transmission signal $\sim\mathcal{E}_1^3\mathcal{E}_2$. Sinusoidal spectral phase shaping strongly affects the TPA, but not the Raman resonances.

physics.chem-ph↗