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Image sensors capable of capturing individual photons have made tremendous progress in recent years. However, this technology faces a major limitation. Because they capture scene information at the individual photon level, the raw data is sparse and noisy. Here we propose CASPI: Collaborative Photon Processing for Active Single-Photon Imaging, a technology-agnostic, application-agnostic, and training-free photon processing pipeline for emerging high-resolution single-photon cameras. By collaboratively exploiting both local and non-local correlations in the spatio-temporal photon data cubes, CASPI estimates scene properties reliably even under very challenging lighting conditions. We demonstrate the versatility of CASPI with two applications: LiDAR imaging over a wide range of photon flux levels, from a sub-photon to high ambient regimes, and live-cell autofluorescence FLIM in low photon count regimes. We envision CASPI as a basic building block of general-purpose photon processing units that will be implemented on-chip in future single-photon cameras.

 

The ubiquitin-binding NBR1 autophagy receptor plays a prominent role in recognizing ubiquitylated protein aggregates for vacuolar degradation by macroautophagy. Here, we show that upon exposing Arabidopsis plants to intense light, NBR1 associates with photodamaged chloroplasts independently of ATG7, a core component of the canonical autophagy machinery. NBR1 coats both the surface and interior of chloroplasts, which is then followed by direct engulfment of the organelles into the central vacuole via a microautophagy-type process. The relocalization of NBR1 into chloroplasts does not require the chloroplast translocon complexes embedded in the envelope but is instead greatly enhanced by removing the self-oligomerization mPB1 domain of NBR1. The delivery of NBR1-decorated chloroplasts into vacuoles depends on the ubiquitin-binding UBA2 domain of NBR1 but is independent of the ubiquitin E3 ligases SP1 and PUB4, known to direct the ubiquitylation of chloroplast surface proteins. Compared to wild-type plants, nbr1 mutants have altered levels of a subset of chloroplast proteins and display abnormal chloroplast density and sizes upon high light exposure. We postulate that, as photodamaged chloroplasts lose envelope integrity, cytosolic ligases reach the chloroplast interior to ubiquitylate thylakoid and stroma proteins which are then recognized by NBR1 for autophagic clearance. This study uncovers a new function of NBR1 in the degradation of damaged chloroplasts by microautophagy. 

New quantitative prognostic markers are needed for improved pancreatic ductal adenocarcinoma (PDAC) prognosis. Second harmonic generation microscopy has been used to show that collagen fiber alignment in PDAC is a negative prognostic factor. In this work, a series of PDAC and normal adjacent tissue (NAT) biopsies were imaged with spatial light interference microscopy (SLIM). Quantitative analysis performed on the biopsy SLIM images show that PDAC fiber structures have lower alignment per unit length, narrower width, and are longer than NAT controls. Importantly, fibrillar collagen in PDAC shows an inverse relationship between survival data and fiber width and length (p < 0.05).

 

Changes in the multi-level physical structure of biological features going from cellular to tissue level composition is a key factor in many major diseases. However, we are only beginning to understand the role of these structural changes because there are few dedicated multiscale imaging platforms with sensitivity at both the cellular and macrostructural spatial scale. A single platform reduces bias and complications from multiple sample preparation methods and can ease image registration. In order to address these needs, we have developed a multiscale imaging system using a range of imaging modalities sensitive to tissue composition: Ultrasound, Second Harmonic Generation Microscopy, Multiphoton Microscopy, Optical Coherence Tomography, and Enhanced Backscattering. This paper details the system design, the calibration for each modality, and a demonstration experiment imaging a rabbit eye.

 

Tissue biopsy evaluation in the clinic is in need of quantitative disease markers for diagnosis and, most importantly, prognosis. Among the new technologies, quantitative phase imaging (QPI) has demonstrated promise for histopathology because it reveals intrinsic tissue nanoarchitecture through the refractive index. However, a vast majority of past QPI investigations have relied on imaging unstained tissues, which disrupts the established specimen processing. Here we present color spatial light interference microscopy (cSLIM) as a new whole-slide imaging modality that performs interferometric imaging on stained tissue, with a color detector array. As a result, cSLIM yields in a single scan both the intrinsic tissue phase map and the standard color bright-field image, familiar to the pathologist. Our results on 196 breast cancer patients indicate that cSLIM can provide stain-independent prognostic information from the alignment of collagen fibers in the tumor microenvironment. The effects of staining on the tissue phase maps were corrected by a mathematical normalization. These characteristics are likely to reduce barriers to clinical translation for the new cSLIM technology.

 

Cerebral aneurysm clips are biomedical implants applied by neurosurgeons to re-approximate arterial vessel walls and prevent catastrophic aneurysmal hemorrhages in patients. Current methods of aneurysm clip production are labor intensive and time-consuming, leading to high costs per implant and limited variability in clip morphology. Metal additive manufacturing is investigated as an alternative to traditional manufacturing methods that may enable production of patient-specific aneurysm clips to account for variations in individual vascular anatomy and possibly reduce surgical complication risks. Relevant challenges to metal additive manufacturing are investigated for biomedical implants, including material choice, design limitations, postprocessing, printed material properties, and combined production methods. Initial experiments with additive manufacturing of 316 L stainless steel aneurysm clips are carried out on a selective laser melting (SLM) system. The dimensions of the printed clips were found to be within 0.5% of the dimensions of the designed clips. Hardness and density of the printed clips (213 ± 7 HV1 and 7.9 g/cc, respectively) were very close to reported values for 316 L stainless steel, as expected. No ferrite and minimal porosity is observed in a cross section of a printed clip, with some anisotropy in the grain orientation. A clamping force of approximately 1 N is measured with a clip separation of 1.5 mm. Metal additive manufacturing shows promise for use in the creation of custom aneurysm clips, but some of the challenges discussed will need to be addressed before clinical use is possible.