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Microalgae are well-known photosynthetic microorganisms used as cell factories for the production of relevant biotechnological compounds. Despite the outstanding characteristics attributed to microalgae, their industrial-scale production still struggles with scale-up problems and economic feasibility. One important bottleneck is the lack of suitable online sensors for the reliable monitoring of biological parameters, mostly concentrations of intracellular components, in microalgae bioprocesses. Software sensors provide an approach to improving the monitoring of those process parameters that are difficult to quantify directly and are therefore only indirectly accessible. Their use aims to improve the productivity of microalgal bioprocesses through better monitoring, control and automation, according to the current demands of Industry 4.0. In this review, a description of the microalgae components of interest as candidates for monitoring in a cultivation, an overview of software sensors, some of the available approaches and tools, and the current state-of-the-art of the design and use of software sensors in microalgae cultivation are presented. The latter is grouped on the basis of measurement methods used as software sensor inputs, employing either optical or non-optical techniques, or a combination of both. Some examples of software sensor design using simulated process data are also given, grouped according to their design, either as model-driven or data-driven estimators.

Current optical health-sensing devices rely on simplified homogeneous tissue models or semi-empirical ratiometric methods, which inadequately address anatomical complexity and inter-individual optical variability. This introduces systematic errors in light propagation modeling, compromising measurement accuracy and clinical robustness, necessitating organ-specific optical models for reliable physiological sensing. To develop a standard optical digital wrist (DW) model by integrating magnetic resonance imaging (MRI) and diffuse optical imaging (DOI), enabling anatomically accurate and optically realistic modeling of wrist tissues for improved precision in wearable optical health monitoring applications. The multimodal MRI-DOI framework was implemented, comprising three key components: (1) statistical integration of high-resolution MRI datasets generated a population-averaged anatomical DW template; (2) region-based time-domain diffuse optical tomography (TD-DOT) with MRI-derived anatomical priors, extracted depth-resolved optical properties of subsurface tissues; (3) spatial frequency domain imaging (SFDI) supplemented high-resolution optical properties of superficial skin layers. Simulation experiments demonstrated the high accuracy of region-based TD-DOT reconstruction, with mean errors below 8.57% ( ) and 9.63% ( ), quantitatively supporting the precision of the proposed approach. Phantom experiments with wrist-mimicking phantoms yielded mean reconstruction errors of 10.52% ( ) and 13.23% ( ) for TD-DOT, and the SFDI top-layer quantification yielded lower errors of 4.48% ( ) and 8.69% ( ), validating the performance of the TD-DOT system and the SFDI system. Furthermore, optical property measurements showed strong agreement with literature values, further validating the reliability and practicality of the methodology. We establish a standard DW template and develop an optical structure acquisition methodology, transitioning biosensing models from homogeneous approximations to anatomically layered models. The approach can enhance the customization, dynamic adaptability, and clinical validity of biosensing technologies.

Tissue optical clearing technology has been developing rapidly in the past decade due to advances in microscopy equipment and various labeling techniques. Consistent modification of primary methods for optical tissue transparency has allowed observation of the whole mouse body at single-cell resolution or thick tissue slices at the nanoscale level, with the final aim to make intact primate and human brains or thick human brain tissues optically transparent. Optical clearance combined with flexible large-volume tissue labeling technology can not only preserve the anatomical structure but also visualize multiple molecular information from intact samples in situ. It also provides a new strategy for studying complex tissues, which is of great significance for deciphering the functional structure of healthy brains and the mechanisms of neurological pathologies. In this review, we briefly introduce the existing optical clearing technology and discuss its application in deciphering connection and structure, brain development, and brain diseases. Besides, we discuss the standard computational analysis tools for large-scale imaging dataset processing and information extraction. In general, we hope that this review will provide a valuable reference for researchers who intend to use optical clearing technology in studying the brain.

Certain topics in research and advancements in medical diagnostics may benefit from improved temporal and spatial resolution during non-invasive optical imaging of living tissue. However, so far no imaging technique can generate entirely diffraction-limited tomographic volumes with a single data acquisition, if the target moves or changes rapidly, such as the human retina. Additionally, the presence of aberrations may represent further difficulties. We show that a simple interferometric setup–based on parallelized optical coherence tomography–acquires volumetric data with 10 billion voxels per second, exceeding previous imaging speeds by an order of magnitude. This allows us to computationally obtain and correct defocus and aberrations resulting in entirely diffraction-limited volumes. As demonstration, we imaged living human retina with clearly visible nerve fiber layer, small capillary networks, and photoreceptor cells. Furthermore, the technique can also obtain phase-sensitive volumes of other scattering structures at unprecedented acquisition speeds.

In today’s clinics, a cell-resolution view of the cornea can be achieved only with a confocal microscope (IVCM) in contact with the eye. Here, we present a common-path full-field/spectral-domain OCT microscope (FF/SD OCT), which enables cell-detail imaging of the entire ocular surface in humans (central and peripheral cornea, limbus, sclera, tear film) without contact and in real-time. Real-time performance is achieved through rapid axial eye tracking and simultaneous defocusing correction. Images contain cells and nerves, which can be quantified over a millimetric field-of-view, beyond the capability of IVCM and conventional OCT. In the limbus, palisades of Vogt, vessels, and blood flow can be resolved with high contrast without contrast agent injection. The fast imaging speed of 275 frames/s (0.6 billion pixels/s) allows direct monitoring of blood flow dynamics, enabling creation of high-resolution velocity maps. Tear flow velocity and evaporation time can be measured without fluorescein administration. Currently a cell-resolution map of the human cornea can only be obtained in the clinic with a confocal microscope in contact with the eye. Here the authors develop a full-field/spectral-domain OCT microscope (FF/SD OCT) to enable cell-level detail of the entire ocular surface, as well as blood flow and tear dynamics.

The purpose of this study was to compare central corneal thickness, thinnest corneal thickness, and the thinnest point of the cornea between Pentacam and anterior segment optical coherence tomography (ASOCT) in patients with dry eye disease (DED). This cross-sectional study included 195 participants between November 2015-June 2017. DED was diagnosed using the Asia Dry Eye Society criteria and further divided into mild and severe DED based on kerato-conjunctival vital staining. Central corneal thickness, thinnest corneal thickness, and the thinnest point of the cornea measured by Pentacam and ASOCT were compared, and Pearson's correlation coefficients were estimated. The differences in central corneal thickness and the thinnest corneal thickness between Pentacam and ASOCT were analysed using Bland-Altman and multivariate regression analyses adjusted for age and sex. This study included 70 non-DED subjects and 52 patients with mild and 73 with severe DED. The Pentacam and ASOCT measurements of central corneal thickness and thinnest corneal thickness were strongly correlated, but the respective values were higher when measured with Pentacam. The Bland-Altman analysis revealed differences in central corneal thickness (non DED, 11.8; mild DED, 13.2; severe DED, 19.6) and in thinnest corneal thickness (non DED, 13.1; mild DED, 13.4; severe DED, 20.7). After adjusting for age and sex, the differences in central corneal thickness (β = 7.029 μm, 95%CI 2.528-11.530) and thinnest corneal thickness (β = 6.958 μm, 95%CI 0.037-13.879) were significantly increased in the severe-DED group. The distribution of the thinnest point of the cornea in the cornea's inferior temporal quadrant between Pentacam and ASOCT deviated in severe DED (Pentacam: 90.4% vs. ASOCT: 83.6%). Clinicians should consider that there were significant differences in corneal-morphology assessment between the measurements with Pentacam and ASOCT in severe DED.

During development, coordinated cell behaviors orchestrate tissue and organ morphogenesis. Detailed descriptions of cell lineages and behaviors provide a powerful framework to elucidate the mechanisms of morphogenesis. To study the cellular basis of limb development, we imaged transgenic fluorescently-labeled embryos from the crustacean Parhyale hawaiensis with multi-view light-sheet microscopy at high spatiotemporal resolution over several days of embryogenesis. The cell lineage of outgrowing thoracic limbs was reconstructed at single-cell resolution with new software called Massive Multi-view Tracker (MaMuT). In silico clonal analyses suggested that the early limb primordium becomes subdivided into anterior-posterior and dorsal-ventral compartments whose boundaries intersect at the distal tip of the growing limb. Limb-bud formation is associated with spatial modulation of cell proliferation, while limb elongation is also driven by preferential orientation of cell divisions along the proximal-distal growth axis. Cellular reconstructions were predictive of the expression patterns of limb development genes including the BMP morphogen Decapentaplegic. During early life, animals develop from a single fertilized egg cell to hundreds, millions or even trillions of cells. These cells specialize to do different tasks; forming different tissues and organs like muscle, skin, lungs and liver. For more than a century, scientists have strived to understand the details of how animal cells become different and specialize, and have created many new techniques and technologies to help them achieve this goal. Limbs – such as arms, legs and wings – form from small lumps of cells called limb buds. Scientists use the shrimp-like crustacean, Parhyale hawaiensis, to study development, including limb growth. This species is useful because it is easy to grow, manipulate and observe its developing young in the laboratory. Understanding how its limbs develop offers important new insights into how limbs develop in other animals too. Wolff, Tinevez, Pietzsch et al. have now combined advanced microscopy with custom computer software, called Massive Multi-view Tracker (MaMuT) to investigate this. As limbs develop in Parhyale, the MaMuT software tracks how cells behave, and how they are organized. This analysis revealed that for cells to produce a limb bud, they need to split at an early stage into separate groups. These groups are organized along two body axes, one that goes from head to tail, and one that runs from back to belly. The limb grows perpendicular to these main body axes, along a new ‘proximal-distal’ axis that goes from nearest to furthest from the body. Wolff et al. found that the cells that contribute to the extremities of the limb divide faster than the ones that stay closer to the body. Finally, the results show that when cells in a limb divide, they mostly divide along the proximal-distal axis, producing one cell that is further from the body than the other. These cell activities may help limbs to get longer as they grow. Notably, the groups of cells seen by Wolff et al. were expressing genes that had previously been identified in developing limbs. This helps to validate the new results and to identify which active genes control the behaviors of the analyzed cells. These findings reveal new ways to study animal development. This approach could have many research uses and may help to link the mechanisms of cell biology to their effects. It could also contribute to new understanding of developmental and genetic conditions that affect human health.

Optimization of regenerative medicine strategies includes the design of biomaterials, development of cell-seeding methods, and control of cell-biomaterial interactions within the engineered tissues. Among these steps, one paramount challenge is to non-destructively image the engineered tissues in their entirety to assess structure, function, and molecular expression. It is especially important to be able to enable cell phenotyping and monitor the distribution and migration of cells throughout the bulk scaffold. Advanced fluorescence microscopic techniques are commonly employed to perform such tasks; however, they are limited to superficial examination of tissue constructs. Therefore, the field of tissue engineering and regenerative medicine would greatly benefit from the development of molecular imaging techniques which are capable of non-destructive imaging of three-dimensional cellular distribution and maturation within a tissue-engineered scaffold beyond the limited depth of current microscopic techniques. In this review, we focus on an emerging depth-resolved optical mesoscopic imaging technique, termed laminar optical tomography (LOT) or mesoscopic fluorescence molecular tomography (MFMT), which enables longitudinal imaging of cellular distribution in thick tissue engineering constructs at depths of a few millimeters and with relatively high resolution. The physical principle, image formation, and instrumentation of LOT/MFMT systems are introduced. Representative applications in tissue engineering include imaging the distribution of human mesenchymal stem cells embedded in hydrogels, imaging of bio-printed tissues, and in vivo applications.