Daniel Rubin, Postdoctoral Faculty Sponsor
- A cascaded nested network for 3T brain MR image segmentation guided by 7T labeling * PATTERN RECOGNITION 2022; 124
Breast Tumor Segmentation in DCE-MRI With Tumor Sensitive Synthesis
IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS
Segmenting breast tumors from dynamic contrast-enhanced magnetic resonance (DCE-MR) images is a critical step for early detection and diagnosis of breast cancer. However, variable shapes and sizes of breast tumors, as well as inhomogeneous background, make it challenging to accurately segment tumors in DCE-MR images. Therefore, in this article, we propose a novel tumor-sensitive synthesis module and demonstrate its usage after being integrated with tumor segmentation. To suppress false-positive segmentation with similar contrast enhancement characteristics to true breast tumors, our tumor-sensitive synthesis module can feedback differential loss of the true and false breast tumors. Thus, by following the tumor-sensitive synthesis module after the segmentation predictions, the false breast tumors with similar contrast enhancement characteristics to the true ones will be effectively reduced in the learned segmentation model. Moreover, the synthesis module also helps improve the boundary accuracy while inaccurate predictions near the boundary will lead to higher loss. For the evaluation, we build a very large-scale breast DCE-MR image dataset with 422 subjects from different patients, and conduct comprehensive experiments and comparisons with other algorithms to justify the effectiveness, adaptability, and robustness of our proposed method.
View details for DOI 10.1109/TNNLS.2021.3129781
View details for Web of Science ID 000732239600001
View details for PubMedID 34874872
In vivo NIR-II structured-illumination light-sheet microscopy.
Proceedings of the National Academy of Sciences of the United States of America
2021; 118 (6)
Noninvasive optical imaging with deep tissue penetration depth and high spatiotemporal resolution is important to longitudinally studying the biology at the single-cell level in live mammals, but has been challenging due to light scattering. Here, we developed near-infrared II (NIR-II) (1,000 to 1,700 nm) structured-illumination light-sheet microscopy (NIR-II SIM) with ultralong excitation and emission wavelengths up to 1,540 and 1,700 nm, respectively, suppressing light scattering to afford large volumetric three-dimensional (3D) imaging of tissues with deep-axial penetration depths. Integrating structured illumination into NIR-II light-sheet microscopy further diminished background and improved spatial resolution by approximately twofold. In vivo oblique NIR-II SIM was performed noninvasively for 3D volumetric multiplexed molecular imaging of the CT26 tumor microenvironment in mice, longitudinally mapping out CD4, CD8, and OX40 at the single-cell level in response to immunotherapy by cytosine-phosphate-guanine (CpG), a Toll-like receptor 9 (TLR-9) agonist combined with OX40 antibody treatment. NIR-II SIM affords an additional tool for noninvasive volumetric molecular imaging of immune cells in live mammals.
View details for DOI 10.1073/pnas.2023888118
View details for PubMedID 33526701
- Light-sheet microscopy in the near-infrared II window NATURE METHODS 2019; 16 (6): 545-+
Light-sheet microscopy in the near-infrared II window.
Non-invasive deep-tissue three-dimensional optical imaging of live mammals with high spatiotemporal resolution is challenging owing to light scattering. We developed near-infrared II (1,000-1,700nm) light-sheet microscopy with excitation and emission of up to approximately 1,320nm and 1,700nm, respectively, for optical sectioning at a penetration depth of approximately 750mum through live tissues without invasive surgery and at a depth of approximately 2mm in glycerol-cleared brain tissues. Near-infrared II light-sheet microscopy in normal and oblique configurations enabled in vivo imaging of live mice through intact tissue, revealing abnormal blood flow and T-cell motion in tumor microcirculation and mapping out programmed-death ligand 1 and programmed cell death protein 1 in tumors with cellular resolution. Three-dimensional imaging through the intact mouse head resolved vascular channels between the skull and brain cortex, and allowed monitoring of recruitment of macrophages and microglia to the traumatic brain injury site.
View details for PubMedID 31086342