Search

Assessment of intratumoral heterogeneity and tumor-host interaction within the tumor microenvironment is becoming increasingly important for innovative cancer therapy decisions because of the unique information it can generate about the state of the disease. However, its assessment and quantification are limited by ambiguous definitions of the tumor-host interface and by human cognitive capacity in current pathology practice. Advances in machine learning and artificial intelligence have opened the field of digital pathology to novel tissue image analytics and feature extraction for generation of high-capacity computational disease management models. A particular benefit is expected from machine-learning applications that can perform extraction and quantification of subvisual features of both intratumoral heterogeneity and tumor microenvironment aspects. These methods generate information about cancer cell subpopulation heterogeneity, potential tumor-host interactions, and tissue microarchitecture, derived from morphologically resolved content using both explicit and implicit features. Several studies have achieved promising diagnostic, prognostic, and predictive artificial intelligence models that often outperform current clinical and pathology criteria. However, further effort is needed for clinical adoption of such methods through development of standardizable high-capacity workflows and proper validation studies.

Over the past two decades, fibrillar collagen reorganization parameters such as the amount of collagen deposition, fiber angle and alignment have been widely explored in numerous studies. These parameters are now widely accepted as stromal biomarkers and linked to disease progression and survival time in several cancer types. Despite all these advances, there has not been a significant effort to make it possible for clinicians to explore these biomarkers without adding steps to the clinical workflow or by requiring high-cost imaging systems. In this paper, we evaluate previously described polychromatic polarization microscope (PPM) to visualize collagen fibers with an optically generated color representation of fiber orientation and alignment when inspecting the sample by a regular microscope with minor modifications. This system does not require stained slides, but is compatible with histological stains such as H&E. Consequently, it can be easily accommodated as part of regular pathology review of tissue slides, while providing clinically useful insight into stromal composition.

Intranuclear birefringent inclusions (IBI) found in various cell types in paraffin-embedded tissue sections have long been considered to be a tissue processing artifact, although an association with biological processes has been suggested. We applied polychromatic polarization microscopy to image their spatial organization. Our study provides evidence that IBI are caused by liquid paraffin-macromolecular crystals formed during paraffin-embedding procedures within cells and potentially reflect an active transcriptional status.

Genomic information must be faithfully transmitted into two daughter cells during mitosis. To ensure the transmission process, interphase chromatin is further condensed into mitotic chromosomes. Although protein factors like condensins and topoisomerase IIα are involved in the assembly of mitotic chromosomes, the physical bases of the condensation process remain unclear. Depletion attraction/macromolecular crowding, an effective attractive force that arises between large structures in crowded environments around chromosomes, may contribute to the condensation process. To approach this issue, we investigated the "chromosome milieu" during mitosis of living human cells using an orientation-independent-differential interference contrast module combined with a confocal laser scanning microscope, which is capable of precisely mapping optical path differences and estimating molecular densities. We found that the molecular density surrounding chromosomes increased with the progression from prophase to anaphase, concurring with chromosome condensation. However, the molecular density went down in telophase, when chromosome decondensation began. Changes in the molecular density around chromosomes by hypotonic or hypertonic treatment consistently altered the condensation levels of chromosomes. In vitro, native chromatin was converted into liquid droplets of chromatin in the presence of cations and a macromolecular crowder. Additional crowder made the chromatin droplets stiffer and more solid-like. These results suggest that a transient rise in depletion attraction, likely triggered by the relocation of macromolecules (proteins, RNAs, and others) via nuclear envelope breakdown and by a subsequent decrease in cell volumes, contributes to mitotic chromosome condensation, shedding light on a different aspect of the condensation mechanism in living human cells. [ABSTRACT FROM AUTHOR]

The pen, or gladius, of the squid is an internalized shell. It serves as a site of attachment for important muscle groups and as a protective barrier for the visceral organs. The pen's durability and flexibility are derived from its unique composition of chitin and protein. We report the characterization of the structure, development, and composition of pens from Doryteuthis pealeii. The nanofibrils of the polysaccharide [beta]-chitin are arranged in an aligned configuration in only specific regions of the pen. Chitin is secreted early in development, enabling us to characterize the changes in pen morphology prior to hatching. The chitin and proteins are assembled in the shell sac surrounded by fluid that has a significantly different ionic composition from squid plasma. Two groups of proteins are associated with the pen: those on its surface and those embedded within the pen. Only 20 proteins are identified as embedded within the pen. Embedded proteins are classified into six groups, including chitin associated, protease, protease inhibitors, intracellular, extracellular matrix, and those that are unknown. The pen proteins share many conserved domains with proteins from other chitinous structures. We conclude that the pen is one of the least complex, load-bearing, chitin-rich structures currently known and is amenable to further studies to elucidate natural construction mechanisms using chitin and protein., Introduction The pen of the squid is considered an internalized shell, homologous to the heavily mineralized external shells of other molluscs (Naef, 1928; Young et al., 1998). Pens are most [...]

Polarising microscopy brought about many advancements in the science of liquid crystals and other soft materials, including those of biological origin. Recent developments in optics and computer-based analysis have enabled a new generation of quantitative polarising microscopy which produces spatial maps of the optic axis. Unfortunately, most of the available approaches require a long acquisition time of multiple images which are then analysed to produce the map. We describe a polychromatic polarising microscope, which allows one to map the patterns of the optical axis in a single-shot exposure, thus enabling a fast temporal resolution. We present a comparative analysis of the new microscope with alternative techniques such as a conventional polarising optical microscope and MicroImager of Hinds Instruments. [ABSTRACT FROM AUTHOR]

We describe a new technique for differential interference contrast (DIC) microscopy, which digitally generates phase gradient images independently of gradient orientation. To prove the principle we investigated specimens recorded at different orientations on a microscope equipped with a precision rotating stage and using regular DIC optics. The digitally generated images successfully displayed and measured phase gradients, independently of gradient orientation. One could also generate images showing distribution of optical path differences or enhanced, regular DIC images with any shear direction. Using special DIC prisms, one can switch the bias and shear directions rapidly without mechanically rotating the specimen or the prisms and orientation-independent DIC images are obtained in a fraction of a second. OCIS codes: 180.0180, 100.2980, 170.1530, 170.3010, 170.3890, 170.3880.

We propose image processing algorithms for measuring two-dimensional distributions of linear birefringence using a pair of variable retarders. Several algorithms that use between two and five recorded frames allow us to optimize measurements for speed, sensitivity, and accuracy. We show images of asters, which consist of radial arrays of microtubule polymers recorded with a polarized light microscope equipped with a universal compensator. Our experimental results confirm our theoretical expectations. The lowest noise level of 0.036 nm was obtained when we used the five-frame technique and four-frame algorithm without extinction setting. The two-frame technique allows us to increase the speed of measurement with acceptable image quality. OCIS codes: 180.0180, 260.1440, 260.2130, 260.5430, 170.1530, 120.5410.