Advances in optical imaging for pharmacological studies

Imaging approaches are an essential tool for following up over time representative parameters of in vivo models, providing useful information in pharmacological studies. Main advantages of optical imaging approaches compared to other imaging methods are their safety, straight-forward use and cost-effectiveness. A main drawback, however, is having to deal with the presence of high scattering and high absorption in living tissues. Depending on how these issues are addressed, three different modalities can be differentiated: planar imaging (including fluorescence and bioluminescence in vivo imaging), optical tomography, and optoacoustic approaches. In this review we describe the latest advances in optical in vivo imaging with pharmacological applications, with special focus on the development of new optical imaging probes in order to overcome the strong absorption introduced by different tissue components, especially hemoglobin, and the development of multimodal imaging systems in order to overcome the resolution limitations imposed by scattering.JR acknowledges support from the EC FP7 CIG grant HIGH-THROUGHPUT TOMO, and MINECO grant FIS 2013-41802-R MESO-IMAGIN

Plenoptic projection fluorescence tomography

A new method to obtain the three-dimensional localization of fluorochrome distributions in micrometric samples is presented. It uses a microlens array coupled to the image port of a standard microscope to obtain tomographic data by a filtered back-projection algorithm. Scanning of the microlens array is proposed to obtain a dense data set for reconstruction. Simulation and experimental results are shown and the implications of this approach in fast 3D imaging are discussed.This work was supported by the Spanish MINECO grant DPI2012-32994. JR acknowledges support from Marie Curie CIG “High-Throughput Tomo” and Spanish MINECO grant FIS2013-41802-R

Recent advances in optical tomography in low scattering media

Low scattering media is the best scenario for optical imaging in thick samples and deep tissue, as it allows to obtain high resolution images without suffering the limitations that the diffusion phenomenon imposes. The high contribution of ballistic light in this regime enabled the development of light sheet microscopy and optical projection tomography, two of the most common techniques nowadays in research laboratories. Their revolutionary approach and wide spectrum of applications and possibilities has lead to a frenetic rhythm of new works and techniques arising every year. The large amount of information available often overwhelms scientists and researchers trying to keep up to date with the last cutting edge advances of the field. This paper aims to give a brief review of the origins and fundamental aspects of these two techniques to focus on the most recent and yet non reviewed works. Apart from novel methods, this document also covers combined multimodal approaches and systems. To conclude, we put a spotlight on the important role that open-source microscopy systems play in the field, as they improve the accessibility to these techniques and promote collaborative networks across the optical imaging community

A comparative study of calibration methods for low-cost ozone sensors in IoT platforms

© 2019 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes,creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.This paper shows the result of the calibration process of an Internet of Things platform for the measurement of tropospheric ozone (O 3 ). This platform, formed by 60 nodes, deployed in Italy, Spain, and Austria, consisted of 140 metal–oxide O 3 sensors, 25 electro-chemical O 3 sensors, 25 electro-chemical NO 2 sensors, and 60 temperature and relative humidity sensors. As ozone is a seasonal pollutant, which appears in summer in Europe, the biggest challenge is to calibrate the sensors in a short period of time. In this paper, we compare four calibration methods in the presence of a large dataset for model training and we also study the impact of a limited training dataset on the long-range predictions. We show that the difficulty in calibrating these sensor technologies in a real deployment is mainly due to the bias produced by the different environmental conditions found in the prediction with respect to those found in the data training phase.Peer ReviewedPostprint (author's final draft

Phase-Retrieved Tomography enables imaging of a Tumor Spheroid in Mesoscopy Regime

Optical tomographic imaging of biological specimen bases its reliability on the combination of both accurate experimental measures and advanced computational techniques. In general, due to high scattering and absorption in most of the tissues, multi view geometries are required to reduce diffuse halo and blurring in the reconstructions. Scanning processes are used to acquire the data but they inevitably introduces perturbation, negating the assumption of aligned measures. Here we propose an innovative, registration free, imaging protocol implemented to image a human tumor spheroid at mesoscopic regime. The technique relies on the calculation of autocorrelation sinogram and object autocorrelation, finalizing the tomographic reconstruction via a three dimensional Gerchberg Saxton algorithm that retrieves the missing phase information. Our method is conceptually simple and focuses on single image acquisition, regardless of the specimen position in the camera plane. We demonstrate increased deep resolution abilities, not achievable with the current approaches, rendering the data alignment process obsolete.Comment: 21 pages, 5 figure

Unleashing Optics and Optoacoustics for Developmental Biology

The past decade marked an optical revolution in biology: an unprecedented number of optical techniques were developed and adopted for biological exploration, demonstrating increasing interest in optical imaging and in vivo interrogations. Optical methods have become faster and have reached nanoscale resolution, and are now complemented by optoacoustic (photoacoustic) methods capable of imaging whole specimens in vivo. Never before were so many optical imaging barriers broken in such a short time-frame: with new approaches to optical microscopy and mesoscopy came an increased ability to image biology at unprecedented speed, resolution, and depth. This review covers the most relevant techniques for imaging in developmental biology, and offers an outlook on the next steps for these technologies and their applications.The work on this review article has received funding from the Deutsche Forschungsgemeinschaft (DFG), Germany (Leibniz Prize 2013; NT 3/10 1) and the Federal Ministry of Education and Research (BMBF), Photonic Science Germany, Tech2See 13N12623/ 4. J.R. acknowledges support from the European Commission FP7 CIG grant HIGH THROUGH PUT TOMO, and Spanish MINECO grant MESO IMAGING FIS2013 41802 R

Use of 13Ca chemical-shifts in protein structure determination

A physics-based method aimed at determining protein structures by using NOE-derived distances together with observed and computed 13C chemical shifts is proposed. The approach makes use of 13Cα chemical shifts, computed at the density functional level of theory, to obtain torsional constraints for all backbone and side-chain torsional angles without making a priori use of the occupancy of any region of the Ramachandran map by the amino acid residues. The torsional constraints are not fixed but are changed dynamically in each step of the procedure, following an iterative self-consistent approach intended to identify a set of conformations for which the computed 13Cα chemical shifts match the experimental ones. A test is carried out on a 76-amino acid, all-α-helical protein; namely, the Bacillus subtilis acyl carrier protein. It is shown that, starting from randomly generated conformations, the final protein models are more accurate than an existing NMR-derived structure model of this protein, in terms of both the agreement between predicted and observed 13Cα chemical shifts and some stereochemical quality indicators, and of similar accuracy as one of the protein models solved at a high level of resolution. The results provide evidence that this methodology can be used not only for structure determination but also for additional protein structure refinement of NMR-derived models deposited in the Protein Data Bank.Fil: Vila, Jorge Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi". Universidad Nacional de San Luis. Facultad de Ciencias Físico, Matemáticas y Naturales. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi"; Argentina. Cornell University; Estados UnidosFil: Ripoll, Daniel R.. Cornell Theory Center; Estados UnidosFil: Scheraga, Harold A.. Cornell University; Estados Unido

Biomedical Applications of Tissue Clearing and Three-Dimensional Imaging in Health and Disease.

Three-dimensional (3D) optical imaging techniques can expand our knowledge about physiological and pathological processes that cannot be fully understood with 2D approaches. Standard diagnostic tests frequently are not sufficient to unequivocally determine the presence of a pathological condition. Whole-organ optical imaging requires tissue transparency, which can be achieved by using tissue clearing procedures enabling deeper image acquisition and therefore making possible the analysis of large-scale biological tissue samples. Here, we review currently available clearing agents, methods, and their application in imaging of physiological or pathological conditions in different animal and human organs. We also compare different optical tissue clearing methods discussing their advantages and disadvantages and review the use of different 3D imaging techniques for the visualization and image acquisition of cleared tissues. The use of optical tissue clearing resources for large-scale biological tissues 3D imaging paves the way for future applications in translational and clinical research.This work was supported by Ministerio de Ciencia, Innovacion y Universidades, ISCIII-FIS grants PI18/00462 co-financed by ERDF, European Union (FEDER) Funds from the European Commission, European Union, ‘‘A way of making Europe’’; the CNIC is supported by theMinisterio de Ciencia, Innovacion y Universidades y the Pro CNIC Foundation, Severo Ochoa Center of Excellence (SEV-2015-0505), CIBER de Salud Mental (CIBERSAM), and COST-action CA16124. J.R. acknowledges funding from EU H2020 FET Open project SENSITIVE, ID 801347, and Ministerio de Ciencia, Innovacion y Universidades Grant FIS2016-77892-RS

Development and testing of a sedation protocol for Neocaridina davidi

Neocaridina davidi, a small freshwater shrimp native to Asia, specifically China, Japan, Korea, and Vietnam, possesses remarkable resistance to poor water quality and offers various advantages over other invertebrate species to examine crucial issues in neuroscience and other related areas. These advantages include robustness, ease of maintenance, and transparency, making them useful for in vivo studies with optical imaging techniques. Despite its suitability for research purposes, particularly in the fields of imaging and fluorescent techniques, the lack of attention given to this species has resulted in the absence of a robust and replicable sedation protocol for immobilization and safe manipulation. Consequently, researchers face challenges in performing experimental procedures while minimizing harm to this specimen. In this study, we have developed and evaluated a simple sedation protocol specifically designed for Neocaridina davidi, assessing its effectiveness using light microscopy and image processing.RF acknowledges funding from Ministerio de Ciencia e Innovación of Spain (project PID2021-123124OB-I00). JR and MM acknowledges funding from the Ministerio de Ciencia e Innovación (PID2020-115088RB-I00, “BEHAVE-3D”). MD acknowledges funding from Instituto de Salud Carlos III through the project DTS22 /00030. This project was co-funded by the European Union (ERDF, “A way to make Europe”), partially supported by Comunidad de Madrid (S2017/BMD-3867 RENIM-CM), and co-financed by European Structural and Investment Fund. The CNIC is supported by Instituto de Salud Carlos III (ISCIII), Ministerio de Ciencia e Innovación (MCIN) and the Pro CNIC Foundation, and is a Severo Ochoa Center of Excellence (SEV-2015-0505)