Chemical Composition and Thermogravimetric Behaviors of Glanded and Glandless Cottonseed Kernels.

Common "glanded" (Gd) cottonseeds contain the toxic compound gossypol that restricts human consumption of the derived products. The "glandless" (Gl) cottonseeds of a new cotton variety, in contrast, show a trace gossypol content, indicating the great potential of cottonseed for agro-food applications. This work comparatively evaluated the chemical composition and thermogravimetric behaviors of the two types of cottonseed kernels. In contrast to the high gossypol content (3.75 g kg-1) observed in Gd kernels, the gossypol level detected in Gl kernels was only 0.06 g kg-1, meeting the FDA's criteria as human food. While the gossypol gland dots in Gd kernels were visually observed, scanning electron microcopy was not able to distinguish the microstructural difference between ground Gd and Gl samples. Chemical analysis and Fourier transform infrared (FTIR) spectroscopy showed that Gl kernels and Gd kernels had similar chemical components and mineral contents, but the former was slightly higher in protein, starch, and phosphorus contents. Thermogravimetric (TG) processes of both kernels and their residues after hexane and ethanol extraction were based on three stages of drying, de-volatilization, and char formation. TG-FTIR analysis revealed apparent spectral differences between Gd and Gl samples, as well as between raw and extracted cottonseed kernel samples, indicating that some components in Gd kernels were more susceptible to thermal decomposition than Gl kernels. The TG and TG-FTIR observations suggested that the Gl kernels could be heat treated (e.g., frying and roasting) at an optimal temperature of 140-150 °C for food applications. On the other hand, optimal pyrolysis temperatures would be much higher (350-500 °C) for Gd cottonseed and its defatted residues for non-food bio-oil and biochar production. The findings from this research enhance the potential utilization of Gd and Gl cottonseed kernels for food applications.

Insights into neurodegeneration from electron microscopy studies.

Neurodegenerative diseases, such as Alzheimer's disease and Parkinson's disease, pose an increasingly severe burden for individuals and society in an ageing population. The causes and mechanisms of the diseases are poorly understood and as yet there are no effective treatments. Some of the molecular complexes involved in degeneration have been identified and electron microscopy has provided an essential tool in the investigations. The focus of this review is to show how electron microscopy has contributed historically to the understanding of disease and to summarize the most striking current advances. It does not seek to cover in detail the recent technical developments in microscopy, involving better microscopes, better electron detectors and more powerful image processing techniques, which have made possible the new insights. In many instances pathological filament assemblies are associated with brain cells that die in the disease, causing the observed symptoms such as dementia or movement disorders. Using electron microscopy it is now possible to go beyond morphological descriptions to produce atomic structures of many of the filaments. This information may help to understand the seeding and assembly of the filaments, with the aim of finding small molecule inhibitors that could potentially provide a form of treatment for the diseases.

Virus Assembly Pathways: Straying Away but Not Too Far.

Non-enveloped RNA viruses pervade all domains of life. In a cell, they co-assemble from viral RNA and capsid proteins. Virus-like particles can form in vitro where virtually any non-cognate polyanionic cargo can be packaged. How only viral RNA gets selected for packaging in vivo, in presence of myriad other polyanionic species, has been a puzzle. Through a combination of charge detection mass spectrometry and cryo-electron microscopy, it is determined that co-assembling brome mosaic virus (BMV) coat proteins and nucleic acid oligomers results in capsid structures and stoichiometries that differ from the icosahedral virion. These previously unknown shell structures are strained and less stable than the native one. However, they contain large native structure fragments that can be recycled to form BMV virions, should a viral genome become available. The existence of such structures suggest the possibility of a previously unknown regulatory pathway for the packaging process inside cells.

Influence of ClearT and ClearT2 Agitation Conditions in the Fluorescence Imaging of 3D Spheroids.

3D tumor spheroids have arisen in the last years as potent tools for the in vitro screening of novel anticancer therapeutics. Nevertheless, to increase the reproducibility and predictability of the data originated from the spheroids it is still necessary to develop or optimize the techniques used for spheroids' physical and biomolecular characterization. Fluorescence microscopy, such as confocal laser scanning microscopy (CLSM), is a tool commonly used by researchers to characterize spheroids structure and the antitumoral effect of novel therapeutics. However, its application in spheroids' analysis is hindered by the limited light penetration in thick samples. For this purpose, optical clearing solutions have been explored to increase the spheroids' transparency by reducing the light scattering. In this study, the influence of agitation conditions (i.e., static, horizontal agitation, and rotatory agitation) on the ClearT and ClearT2 methods' clearing efficacy and tumor spheroids' imaging by CLSM was characterized. The obtained results demonstrate that the ClearT method results in the improved imaging of the spheroids interior, whereas the ClearT2 resulted in an increased propidium iodide mean fluorescence intensity as well as a higher signal depth in the Z-axis. Additionally, for both methods, the best clearing results were obtained for the spheroids treated under the rotatory agitation. In general, this work provides new insights on the ClearT and ClearT2 clearing methodologies and their utilization for improving the reproducibility of the data obtained through the CLSM, such as the analysis of the cell death in response to therapeutics administration.

A miniaturized, tethered, spectrally-encoded confocal endomicroscopy capsule.

BACKGROUND AND OBJECTIVE: The tethered spectrally-encoded confocal endomicroscopy (SECM) capsule is an imaging device that once swallowed by an unsedated patient can visualize cellular morphologic changes associated with gastrointestinal (GI) tract diseases in vivo. Recently, we demonstrated a tethered SECM capsule for counting esophageal eosinophils in patients with eosinophilic esophagitis (EoE) in vivo. Yet, the current tethered SECM capsule is far too long to be widely utilized for imaging pediatric patients, who constitute a major portion of the EoE patient population. In this paper, we present a new tethered SECM capsule that is 33% shorter, has an easier and repeatable fabrication process, and produces images with reduced speckle noise. MATERIALS AND METHODS: The smaller SECM capsule utilized a miniature condenser to increase the fiber numerical aperture and reduce the capsule length. A custom 3D-printed holder was developed to enable easy and repeatable device fabrication. A dual-clad fiber (DCF) was used to reduce speckle noise. RESULTS: The fabricated SECM capsule (length = 20 mm; diameter = 7 mm) had a similar size and shape to a pediatric dietary supplement pill. The new capsule achieved optical sectioning thickness of 13.2 µm with a small performance variation between devices of 1.7 µm. Confocal images of human esophagus obtained in vivo showed the capability of this new device to clearly resolve microstructural epithelial details with reduced speckle noise. CONCLUSIONS: We expect that the smaller size and better image performance of this new SECM capsule will greatly facilitate the clinical adoption of this technology in pediatric patients and will enable more accurate assessment of EoE-suspected tissues. Lasers Surg. Med. 51:452-458, 2019. © 2019 Wiley Periodicals, Inc.

Application of fluorescence lifetime imaging microscopy of DNA binding dyes to assess radiation-induced chromatin compaction changes.

In recent years several approaches have been developed to address the chromatin status and its changes in eukaryotic cells under different conditions-but only few are applicable in living cells. Fluorescence lifetime imaging microscopy (FLIM) is a functional tool that can be used for the inspection of the molecular environment of fluorophores in living cells. Here, we present the use of single organic minor groove DNA binder dyes in FLIM for measuring chromatin changes following modulation of chromatin structure in living cells. Treatment with histone deacetylase inhibitors led to an increased fluorescence lifetime indicating global chromatin decompaction, whereas hyperosmolarity decreased the lifetime of the used dyes, thus reflecting the expected compaction. In addition, we demonstrate that time domain FLIM data based on single photon counting should be optimized using pile-up and counting loss correction, which affect the readout even at moderate average detector count rates in inhomogeneous samples. Using these corrections and utilizing Hoechst 34580 as chromatin compaction probe, we measured a pan nuclear increase in the lifetime following irradiation with X-rays in living NIH/3T3 cells thus providing a method to measure radiation-induced chromatin decompaction.

Large-area spectrally encoded confocal endomicroscopy of the human esophagus in vivo.

BACKGROUND AND OBJECTIVE: Diagnosis of esophageal diseases is often hampered by sampling errors that are inherent in endoscopic biopsy, the standard of care. Spectrally encoded confocal microscopy (SECM) is a high-speed reflectance confocal endomicroscopy technology that has the potential to visualize cellular features from large regions of the esophagus, greatly decreasing the likelihood of sampling error. In this paper, we report results from a pilot clinical study imaging the human esophagus in vivo with a prototype SECM endoscopic probe. MATERIALS AND METHODS: In this pilot clinical study, six patients undergoing esophagogastroduodenoscopy (EGD) for surveillance of Barrett's esophagus (BE) were imaged with the SECM endoscopic probe. The device had a diameter of 7 mm, a length of 2 m, and a rapid-exchange guide wire provision for esophageal placement. During EGD, the distal portion of the esophagus of each patient was sprayed with 2.5% acetic acid to enhance nuclear contrast. The SECM endoscopic probe was then introduced over the guide wire to the distal esophagus and large-area confocal images were obtained by helically scanning the optics within the SECM probe. RESULTS: Large area confocal images of the distal esophagus (image length = 4.3-10 cm; image width = 2.2 cm) were rapidly acquired at a rate of ∼9 mm2 /second, resulting in short procedural times (1.8-4 minutes). SECM enabled the visualization of clinically relevant architectural and cellular features of the proximal stomach and normal and diseased esophagus, including squamous cell nuclei, BE glands, and goblet cells. CONCLUSIONS: This study demonstrates that comprehensive spectrally encoded confocal endomicroscopy is feasible and can be used to visualize architectural and cellular microscopic features from large segments of the distal esophagus at the gastroesophageal junction. By providing microscopic images that are less subject to sampling error, this technology may find utility in guiding biopsy and planning and assessing endoscopic therapy. Lasers Surg. Med. 49:233-239, 2017. © 2016 Wiley Periodicals, Inc.

First haplosporidan parasite reported infecting a member of the Superfamily Pinnoidea (Pinna nobilis) during a mortality event in Alicante (Spain, Western Mediterranean).

Several stages of a haplosporidan parasite, including spores, were detected infecting three out of four specimens of the Pen Shell Pinna nobilis from the coast of Alicante (Western Mediterranean). A mortality event initiated few weeks before the sampling. The infection was systemic in the connective tissue, with free uni-nucleate stages and early plasmodia, whereas sporulation process took place in the digestive tubules disrupting them. Morphological details, by light and transmission electron microscopy, and PCR amplification confirmed that the parasite belongs to the haplosporidan group. Spores were pleomorphic, usually elongated ovoid, with round to elongated haplosporosomes-like in the sporoplasma. The operculum was situated in the apical zone of the wall, with an external lid, and the nucleus tended to be eccentric in the basal zone. Spore ornamentation was not observed. The single uninfected specimen appeared to be healthy. This is the first report of a haplosporidan parasite infecting a member of the Superfamily Pinnoidea and this is the first histopathological study of a mortality event in the endangered and protected P. nobilis.

Dynamical Observation and Detailed Description of Catalysts under Strong Metal-Support Interaction.

Understanding the structures of catalysts under realistic conditions with atomic precision is crucial to design better materials for challenging transformations. Under reducing conditions, certain reducible supports migrate onto supported metallic particles and create strong metal-support states that drastically change the reactivity of the systems. The details of this process are still unclear and preclude its thorough exploitation. Here, we report an atomic description of a palladium/titania (Pd/TiO2) system by combining state-of-the-art in situ transmission electron microscopy and density functional theory (DFT) calculations with structurally defined materials, in which we visualize the formation of the overlayers at the atomic scale under atmospheric pressure and high temperature. We show that an amorphous reduced titania layer is formed at low temperatures, and that crystallization of the layer into either mono- or bilayer structures is dictated by the reaction environment and predicted by theory. Furthermore, it occurs in combination with a dramatic reshaping of the metallic surface facets.

Cost-effective elimination of lipofuscin fluorescence from formalin-fixed brain tissue by white phosphor light emitting diode array.

Autofluorescence of aldehyde-fixed tissues greatly hinders fluorescence microscopy. In particular, lipofuscin, an autofluorescent component of aged brain tissue, complicates fluorescence imaging of tissue in neurodegenerative diseases. Background and lipofuscin fluorescence can be reduced by greater than 90% through photobleaching using white phosphor light emitting diode arrays prior to treatment with fluorescent probes. We compared the effect of photobleaching versus established chemical quenchers on the quality of fluorescent staining in formalin-fixed brain tissue of frontotemporal dementia with tau-positive inclusions. Unlike chemical quenchers, which reduced fluorescent probe signals as well as background, photobleaching treatment had no effect on probe fluorescence intensity while it effectively reduced background and lipofuscin fluorescence. The advantages and versatility of photobleaching over established methods are discussed.

Evaluation of the Cytotoxic Behavior of Fungal Extracellular Synthesized Ag Nanoparticles Using Confocal Laser Scanning Microscope.

Silver nanoparticles have been synthesized by subjecting a reaction medium to a Fusarium oxysporum biomass at 28 °C for 96 h. The biosynthesized Ag nanoparticles were characterized on the basis of their anticipated peak at 405 nm using UV-Vis-NIR spectroscopy. Structural confirmation was evident from the characteristic X-ray diffraction (XRD) pattern, high-resolution transmission electron Microscopy (HRTEM) and the particle size analyzer. The Ag nanoparticles were of dimension 40 ± 5 nm and spherical in shape. The study mainly focused on using the confocal laser scanning microscope (CLSM) to examine the cytotoxic activities of fungal synthesized Ag nanoparticles on a human breast carcinoma cell line MCF7 cell, which featured remarkable vacuolation, thus indicating a potent cytotoxic activity.

Homologous Hevea brasiliensis REF (Hevb1) and SRPP (Hevb3) present different auto-assembling.

HbREF and HbSRPP are two Hevea brasiliensis proteins present on rubber particles, and probably involved in the coagulation of latex. Their function is unclear, but we previously discovered that REF had amyloid properties, which could be of particular interest during the coagulation process. First, we confirmed that REF and SRPP, homologous and principal proteins in hevea latex, are not glycoproteins. In this work, we investigated various aspects of protein interactions: aggregation, auto-assembling, yeast and erythrocyte agglutination, co-interactions by various biochemical (PAGE, spectroscopy, microscopy), biophysical (DLS, ellipsometry) and structural (TEM, ATR-FTIR, PM-IRRAS) approaches. We demonstrated that both proteins are auto-assembling into different aggregative states: REF polymerizes as an amyloid rich in ß-sheets and forms quickly large aggregates (>µm), whereas SRPP auto-assembles in solution into stable nanomultimers of a more globular nature. Both proteins are however able to interact together, and SRPP may inhibit the amyloidogenesis of REF. REF is also able to interact with the membranes of yeasts and erythrocytes, leading to their agglutination. In addition, we also showed that both REF and SRPP did not have antimicrobial activity, whereas their activity on membranes has been clearly evidenced. We may suspect that these aggregative properties, even though they are clearly different, may occur during coagulation, when the membrane is destabilized. The interaction of proteins with membranes could help in the colloidal stability of latex, whereas the protein-protein interactions would contribute to the coagulation process, by bringing rubber particles together or eventually disrupting the particle monomembranes.

Multichannel conductance of folded single-molecule wires aided by through-space conjugation.

Deciphering charge transport through multichannel pathways in single-molecule junctions is of high importance to construct nanoscale electronic devices and deepen insight into biological redox processes. Herein, we report two tailor-made folded single-molecule wires featuring intramolecular π-π stacking interactions. The scanning tunneling microscope (STM) based break-junction technique and theoretical calculations show that through-bond and through-space conjugations are integrated into one single-molecule wire, allowing for two simultaneous conducting channels in a single-molecule junction. These folded molecules with stable π-π stacking interaction offer conceptual advances in single-molecule multichannel conductance, and are perfect models for conductance studies in biological systems, organic thin films, and π-stacked columnar aggregates.

Understanding and Mitigating Lattice Collapse Degradation in Layered Oxide Materials for Sodium-Ion Battery Anode.

Na2Ti3O7 has attracted significant attention due to its ecofriendliness and cost-effectiveness for sodium-ion batteries. However, their limited cycling stability hampers their practical applications. Herein, we elucidate a mechanism of structural degradation caused by the heterogeneous phase transition in the Na2Ti3O7 anode using aberration-corrected (scanning) transmission electron microscopy (S)TEM and in situ TEM. It is found that the unevenly distributed phase transition results in the accumulation of strain, which promotes the growth of microcracks and eventually leads to structural decomposition and electrochemical failure. Motivated by this degradation mechanism, nanowires were proposed, and the structural stability is thus improved with the lattice strain effectively released. These findings deepen our understanding of ion transport and degradation mechanisms in intercalated layered electrode materials while emphasizing the significance of the material structure engineered for improving electrode performance.

Characterization of microthermal zones induced by fractional radiofrequency using reflectance confocal microscopy: a preliminary study.

BACKGROUND: The microthermal zone (MTZ) produced by fractional device have been mostly evaluated through histopathologic analysis. Study of ablative type MTZ created by fractional device and skin thermal interaction using in vivo reflectance confocal microscopy (RCM) has been rarely reported. OBJECTIVES: We evaluated the in vivo human RCM skin images of ablated fractional radiofrequency (RF) treatment to demonstrate the thermal interaction between RF and skin tissue. SUBJECTS AND METHOD: Three healthy male subjects underwent a single irradiation of fractional RF on the upper back area. The diameter, area, and depth of the MTZ was measured using RCM. Three female domestic swine were used for comparative histopathological study. RESULTS: After RF treatment, crusted holes surrounding pale edematous rings were visible in RCM images. The empty spaces correlated to the location of ablative channels, and the presence of thermal modification zones corresponded to areas with a whitish ring showing high reflectance. Ablation depth increased in proportion to the energy of fractional RF. However, the diameter of the thermal modified zone was relatively constant regardless of RF energy. CONCLUSIONS: RCM successfully identified in vivo acute thermal changes after fractional RF. The results obtained in this study provide a clearer picture of tissue-thermal interactions in the skin.

Initial Formulation of Novel Peanut Butter-like Products from Glandless Cottonseed.

Glandless (Gl) cottonseed is a unique cotton variety with only a trace content of toxic gossypol present. This new cottonseed raises the potential of its enhanced utilization as an agro-food for human consumption. In this work, Gl cottonseed kernels were used with additional cottonseed oil to produce novel peanut butter-like products. Kernels roasted at two temperatures (140 or 150 °C) for a given time (15 or 30 min) were first ground with different ratios of cottonseed oil and two other ingredients (i.e., salt and sugar) with a food blender, and then passed through a meat grinder with a 4-mm-hole grinding plate. Per the preliminary result, the butter-like products with Gl kernels roasted at 150 °C were subject to further structural and textural evaluation. The color of the two butter-like products was comparable to a commercial peanut butter, but the formers' textural properties were significantly different (p ≤ 0.05) from the latter. Morphologic examination by Scanning Electron Microscopy (SEM) and cryo-SEM revealed that the butter product with a longer (30 min) roasting time possessed a smoother surface than the products with a shorter (15 min) roasting time. Oil stability test showed no substantial oil separation (<3%) from the butter products over 7 weeks at ambient temperature (22 °C). This work provides the basic information and parameters for lab cottonseed butter making so that optimization and characterization of cottonseed butter formation can be designed and performed in future research.

Sorption-oxidation mechanism for the removal of arsenic (III) using Cu-doped ZnO in an alkaline medium.

1-D oxides Zn1-xCuxO and spherical composites Zn1-xCuxO/CuO were obtained by thermolysis of formate-glycolate complexes Zn1-xCux (HCOO)(OCH2CH2O)1/2 (0 ≤ x ≤ 0.15). The structural and property characteristics showed that Cu was introduced into the Zn site of the ZnO lattice to form the Zn0.95Cu0.05O solid solution. The concentration of copper in the precursors regulates the topological and structural features of the formation of Zn1-xCuxO oxides, which determine their sorption and photocatalytic properties. The materials were tested in As3+ photooxidation reaction under UV and visible radiation. It has been established that Cu+ is an effective dopant in the composition of 1-D oxide Zn1-xCuxO (0 ≤ x < 0.1). The presence of Cu2+ in the shell of Zn1-xCuxO/CuO composite reduces the photoactivity of the material. The maximum efficiency of arsenic extraction (up to 80% for Zn0.95Cu0.05O) was achieved from dilute arsenic-containing solutions (3.8 mg/L As) and an adsorbent concentration of 0.8 g/L for 24 h. In saturated solutions (380 mg/L As) this value is reduced by a factor of 100. According to XPS data, the primary process is As3+ sorption on the catalyst surface followed by its oxidation to As5+. Using the EPR method it was found that singly charged oxygen vacancies V O + $$ {V}_O^{+} $$ associated with Cu in Zn1-xCuxO are directly involved in the photostimulated oxidation of As3+. PRACTITIONER POINTS: Two types of Zn1-x Cux O photocatalysts were obtained by thermolysis of the Zn1-x Сux (HCOO)(OCH2 CH2 O)1/2 complex (0 ≤ x ≤ 0.15) in air. Sorption of arsenic from dilute solutions reaches 80% on 1-D oxide Zn0.95 Cu0.05 O. Sorption of As3+ on the catalyst surface is at primary process followed by its oxidation to As5+ . Removal of As3+ from alkaline solutions occurs due to successful combination of sorption and photocatalytic properties of the 1-D oxides Zn1-x Cux O.

The diagnostic utility of microscopic quality assessment of sputum samples in the era of rapid syndromic PCR testing.

This prospective study assessed the value of initial microscopy evaluation of sputum samples submitted for rapid syndromic PCR-based testing. Bacterial detections by the BioFire FilmArray Pneumonia Panel plus in 126 high- and 108 low-quality sputum samples, based on initial microscopy evaluation in samples from patients with lower respiratory tract infections were compared. We found that high-quality samples had a higher proportion of bacterial detections compared to low-quality samples (P = 0.013). This included a higher proportion of detections of bacteria deemed clinically relevant by predefined criteria (70% and 55%, P = 0.016), as well as a higher proportion of detections of Haemophilus influenzae (36% and 20%, P = 0.010). High-quality samples also had more detections of bacteria with high semi-quantitative values. The study found no significant difference between high- and low-quality samples in the proportions of samples with a single species of bacteria detected, samples with a bacteria treated by the clinician, samples with detection of a proven etiology of community-acquired pneumonia by predefined criteria, the number of bacterial species detected, or the detection of Streptococcus pneumoniae, Moraxella catarrhalis, or Staphylococcus aureus. The results showed that 40% (95% CI 35%-47%) of the bacterial detections would have been missed if only high-quality samples were analyzed. This included 41% (27%-56%) of detections of S. pneumoniae, 33% (23%-45%) of detections of H. influenzae, 42% (28%-58%) of detections of S. aureus, and 37% (23%-54%) of detections of M. catarrhalis. These findings suggest that all sputum samples submitted for rapid syndromic PCR testing should be analyzed, regardless of initial microscopy quality assessment. (This study has been registered at ClinicalTrials.gov under registration no. NCT04660084.) IMPORTANCE Microscopic quality assessment of sputum samples was originally designed for sputum culture, and its applicability in today's workflow, which includes syndromic PCR testing, may differ. Addressing this crucial gap, our study emphasizes the need to optimize the use and workflow of syndromic PCR panels, like the BioFire FilmArray Pneumonia plus (FAP plus), in microbiology laboratories. These advanced PCR-based tests offer rapid and comprehensive pathogen detection for respiratory infections, yet their full potential remains uncertain. By comparing bacterial detections in high- and low-quality sputum samples, we underscore the importance of including low-quality samples in testing. Our findings reveal a significant proportion of potentially clinically relevant bacterial detections that would have been missed if only high-quality samples were analyzed. These insights support the efficient implementation of syndromic PCR panels, ultimately enhancing patient care and outcomes.

High- and Super-Resolution Imaging of Cell-Cell Interfaces.

Physical interfaces mediate interactions between multiple types of cells. Despite the importance of such interfaces to the cells' function, their high-resolution optical imaging has been typically limited due to poor alignment of the interfaces relative to the optical plane of imaging. Here, we present a simple and robust method to align cell-cell interfaces in parallel to the coverslip by adhering the interacting cells to two opposing coverslips and bringing them into contact in a controlled and stable fashion. We demonstrate aberration-free high-resolution imaging of interfaces between live T cells and antigen-presenting cells, known as immune synapses, as an outstanding example. Imaging methods may include multiple diffraction-limited and super-resolution microscopy techniques (e.g., bright-field, confocal, STED, and dSTORM). Thus, our simple and widely compatible approach allows imaging with high- and super-resolution the intricate structure and molecular organization within a variety of cell-cell interfaces.

Serial intravital 2-photon microscopy and analysis of the kidney using upright microscopes.

Serial intravital 2-photon microscopy of the kidney and other abdominal organs is a powerful technique to assess tissue function and structure simultaneously and over time. Thus, serial intravital microscopy can capture dynamic tissue changes during health and disease and holds great potential to characterize (patho-) physiological processes with subcellular resolution. However, successful image acquisition and analysis require significant expertise and impose multiple potential challenges. Abdominal organs are rhythmically displaced by breathing movements which hamper high-resolution imaging. Traditionally, kidney intravital imaging is performed on inverted microscopes where breathing movements are partly compensated by the weight of the animal pressing down. Here, we present a custom and easy-to-implement setup for intravital imaging of the kidney and other abdominal organs on upright microscopes. Furthermore, we provide image processing protocols and a new plugin for the free image analysis software FIJI to process multichannel fluorescence microscopy data. The proposed image processing pipelines cover multiple image denoising algorithms, sample drift correction using 2D registration, and alignment of serial imaging data collected over several weeks using landmark-based 3D registration. The provided tools aim to lower the barrier of entry to intravital microscopy of the kidney and are readily applicable by biomedical practitioners.