Full-aperture extended-depth oblique plane microscopy through dynamic remote focusing

Significance

The reprojection setup typical of oblique plane microscopy (OPM) limits the effective aperture of the imaging system, and therefore its efficiency and resolution. Large aperture system is only possible through the use of custom specialized optics. A full-aperture OPM made with off the shelf components would both improve the performance of the method and encourage its widespread adoption.

Aim

To prove the feasibility of an OPM without a conventional reprojection setup, retaining the full aperture of the primary objective employed.

Approach

A deformable lens based remote focusing setup synchronized with the rolling shutter of a complementary metal-oxide semiconductor detector is used instead of a traditional reprojection system.

Results

The system was tested on microbeads, prepared slides, and zebrafish embryos. Resolution and pixel throughput were superior to conventional OPM with cropped apertures, and comparable with OPM implementations with custom made optical components.

Conclusions

An easily reproducible approach to OPM imaging is presented, eliminating the conventional reprojection setup and exploiting the full aperture of the employed objective.

Rapid alkalinization factor 22 has a structural and signalling role in root hair cell wall assembly

Pressurized cells with strong walls make up the hydrostatic skeleton of plants. Assembly and expansion of such stressed walls depend on a family of secreted RAPID ALKALINIZATION FACTOR (RALF) peptides, which bind both a membrane receptor complex and wall-localized LEUCINE-RICH REPEAT EXTENSIN (LRXs) in a mutually exclusive way. Here we show that, in root hairs, the RALF22 peptide has a dual structural and signalling role in cell expansion. Together with LRX1, it directs the compaction of charged pectin polymers at the root hair tip into periodic circumferential rings. Free RALF22 induces the formation of a complex with LORELEI-LIKE-GPI-ANCHORED PROTEIN 1 and FERONIA, triggering adaptive cellular responses. These findings show how a peptide simultaneously functions as a structural component organizing cell wall architecture and as a feedback signalling molecule that regulates this process depending on its interaction partners. This mechanism may also underlie wall assembly and expansion in other plant cell types.

Fast data fitting scheme for compressive multispectral fluorescence lifetime imaging

A single-pixel camera combined with compressive sensing techniques is a promising fluorescence microscope scheme for acquiring a multidimensional dataset (space, spectrum, and lifetime) and for reducing the measurement time with respect to conventional microscope schemes. However, upon completing the acquisition, a computational step is necessary for image reconstruction and data analysis, which can be time-consuming, potentially canceling out the beneficial effect of compressive sensing. In this work, we propose and experimentally validate a fast-fit workflow based on global analysis and multiple linear fits, which significantly reduces the computation time from tens of minutes to less than 1 s. Moreover, as the method is interlaced with the measurement flow, it can be applied in parallel with the acquisitions.

The Role of the Anterior Thalamic Nuclei in the Genesis of Memory Disorders in Alzheimer's Disease: An Exploratory Study

BACKGROUND

Increasing evidence is demonstrating that degeneration of specific thalamic nuclei, in addition to the hippocampus, may occur in Alzheimer's disease (AD) from the prodromal stage (mild cognitive impairment - MCI) and contribute to memory impairment.

OBJECTIVE

Here, we evaluated the presence of macro and micro structural alterations at the level of the anterior thalamic nuclei (ATN) and medio-dorsal thalamic nuclei (MDTN) in AD and amnestic MCI (aMCI) and the possible relationship between such changes and the severity of memory impairment.

METHODS

For this purpose, a sample of 50 patients with aMCI, 50 with AD, and 50 age- and education-matched healthy controls (HC) were submitted to a 3-T MRI protocol with whole-brain T1-weighted and diffusion tensor imaging and a comprehensive neuropsychological assessment.

RESULTS

At macro-structural level, both the ATN and MDTN were found significantly smaller in patients with aMCI and AD when compared to HC subjects. At micro-structural level, instead, diffusion alterations that significantly differentiated aMCI and AD patients from HC subjects were found only in the ATN, but not in the MDTN. Moreover, diffusion values of the ATN were significantly associated with poor episodic memory in the overall patients' group.

CONCLUSIONS

These findings represent the first in vivo evidence of a relevant involvement of ATN in the AD-related neurodegeneration and memory profile and strengthen the importance to look beyond the hippocampus when considering neurological conditions characterized by memory decline.

Noninvasive In Planta Live Measurements of H2O2 and Glutathione Redox Potential with Fluorescent roGFPs-Based Sensors

In this protocol, we present a noninvasive in planta bioimaging technique for the analysis of hydrogen peroxide (H2O2) and glutathione redox potential in adult Arabidopsis thaliana plants. The technique is based on the use of stereo fluorescence microscopy to image A. thaliana plants expressing the two genetically encoded fluorescent sensors roGFP2-Orp1 and Grx1-roGFP2. We provide a detailed step-by-step protocol for performing low magnification imaging with mature plants grown in soil or hydroponic systems. This protocol aims to serve the scientific community by providing an accessible approach to noninvasive in planta bioimaging and data analysis.

Structured-light-sheet imaging in an integrated optofluidic platform

Heterogeneity investigation at the single-cell level reveals morphological and phenotypic characteristics in cell populations. In clinical research, heterogeneity has important implications in the correct detection and interpretation of prognostic markers and in the analysis of patient-derived material. Among single-cell analysis, imaging flow cytometry allows combining information retrieved by single cell images with the throughput of fluidic platforms. Nevertheless, these techniques might fail in a comprehensive heterogeneity evaluation because of limited image resolution and bidimensional analysis. Light sheet fluorescence microscopy opened new ways to study in 3D the complexity of cellular functionality in samples ranging from single-cells to micro-tissues, with remarkably fast acquisition and low photo-toxicity. In addition, structured illumination microscopy has been applied to single-cell studies enhancing the resolution of imaging beyond the conventional diffraction limit. The combination of these techniques in a microfluidic environment, which permits automatic sample delivery and translation, would allow exhaustive investigation of cellular heterogeneity with high throughput image acquisition at high resolution. Here we propose an integrated optofluidic platform capable of performing structured light sheet imaging flow cytometry (SLS-IFC). The system encompasses a multicolor directional coupler equipped with a thermo-optic phase shifter, cylindrical lenses and a microfluidic network to generate and shift a patterned light sheet within a microchannel. The absence of moving parts allows a stable alignment and an automated fluorescence signal acquisition during the sample flow. The platform enables 3D imaging of an entire cell in about 1 s with a resolution enhancement capable of revealing sub-cellular features and sub-diffraction limit details.

Model-based deep learning framework for accelerated optical projection tomography

In this work, we propose a model-based deep learning reconstruction algorithm for optical projection tomography (ToMoDL), to greatly reduce acquisition and reconstruction times. The proposed method iterates over a data consistency step and an image domain artefact removal step achieved by a convolutional neural network. A preprocessing stage is also included to avoid potential misalignments between the sample center of rotation and the detector. The algorithm is trained using a database of wild-type zebrafish (Danio rerio) at different stages of development to minimise the mean square error for a fixed number of iterations. Using a cross-validation scheme, we compare the results to other reconstruction methods, such as filtered backprojection, compressed sensing and a direct deep learning method where the pseudo-inverse solution is corrected by a U-Net. The proposed method performs equally well or better than the alternatives. For a highly reduced number of projections, only the U-Net method provides images comparable to those obtained with ToMoDL. However, ToMoDL has a much better performance if the amount of data available for training is limited, given that the number of network trainable parameters is smaller.

Large field of view aberrations correction with deformable lenses and multi conjugate adaptive optics

Optical microscopes can have limited resolution due to aberrations caused by samples and sample holders. Using deformable mirrors and wavefront sensorless optimization algorithms can correct these aberrations, but the correction is limited to a small area of the field of view. This study presents an adaptive optics method that uses a series of plug-and-play deformable lenses for large field of view wavefront correction. A direct wavefront measurement method using the spinning sub-pupil aberration measurement technique is combined with correction based on the deformable lenses. Experimental results using fluorescence microscopy with a wide field and a light sheet fluorescence microscope show that the proposed method can achieve detection and correction over an extended field of view with a compact transmissive module placed in the detection path of the microscope. This method could improve the resolution and accuracy of imaging in a variety of fields, including biology and materials science.

Versatile Microfluidics for Biofabrication Platforms Enabled by an Agile and Inexpensive Fabrication Pipeline

Microfluidics have transformed diagnosis and screening in regenerative medicine. Recently, they are showing much promise in biofabrication. However, their adoption is inhibited by costly and drawn-out lithographic processes thus limiting progress. Here, multi-material fibers with complex core-shell geometries with sizes matching those of human arteries and arterioles are fabricated employing versatile microfluidic devices produced using an agile and inexpensive manufacturing pipeline. The pipeline consists of material extrusion additive manufacturing with an innovative continuously varied extrusion (CONVEX) approach to produce microfluidics with complex seamless geometries including, novel variable-width zigzag (V-zigzag) mixers with channel widths ranging from 100-400 µm and hydrodynamic flow-focusing components. The microfluidic systems facilitated rapid mixing of fluids by decelerating the fluids at specific zones to allow for increased diffusion across the interfaces. Better mixing even at high flow rates (100-1000 µL min-1 ) whilst avoiding turbulence led to high cell cytocompatibility (>86%) even when 100 µm nozzles are used. The presented 3D-printed microfluidic system is versatile, simple and efficient, offering a great potential to significantly advance the microfluidic platform in regenerative medicine.

Narrative discourse production in Parkinson's disease: Decoupling the role of cognitive-linguistic and motor speech changes

Introduction

the interplay between neuropsychological and communicative abilities in Parkinson's disease (PD) has been relatively overlooked, and it is not entirely understood which difficulties are consequent to impaired motor control, and which have a linguistic/cognitive basis. Here, we examined narrative discourse in PD using a multi-level analysis procedure considering sentence-level (productivity, lexical-grammatical processing) and discourse-level processes (narrative organization, informativeness), and partialling out patients' motor speech impairments. The interaction between cognitive (i.e. linguistic and executive) and communication abilities was also investigated.

Methods

Twenty-nine PD subjects in the mild stage of the disease were compared to 29 matched healthy comparators (HC) on quantitative measures of narrative discourse derived from two picture description tasks. Multivariate (considering articulation rate and educational attainment as covariates) and univariate (with group membership as independent variable) analyses of variance were conducted on separate linguistic domains. The contribution of executive/linguistic abilities to PD's narrative performance was explored by multiple regression analyses on narrative measures significantly differentiating patients from HC.

Results

significant reductions in patients were observed on measures of productivity (less well-formed words, shorter sentences) and informativeness (fewer conceptual units, less informative elements, lower number of details) and these alterations were explained by variations in linguistic abilities (action and object naming) rather than executive abilities. Articulation rate and educational attainment did not impact the observed reduced productivity and under-informativeness.

Conclusion

referential narrative discourse is altered in PD, regardless of motor impairments in speech production. The observed reductions in productivity/informativeness aspects of narratives were related to naming abilities and in particular to verbs processing, consistently with the neurocognitive model of motor language coupling. Since narratives are amenable to recurrent and automated analysis for the identification of linguistic patterns potentially anticipating the development of PD and the onset of cognitive deterioration, discourse abilities should be quantitatively and repeatedly profiled in the disorder.

A Bayesian-adaptive decision-theoretic approach can reduce the sample sizes for multiarm exercise oncology trials

OBJECTIVES

Adaptive designs may reduce trial sample sizes and costs. This study illustrates a Bayesian-adaptive decision-theoretic design applied to a multiarm exercise oncology trial.

STUDY DESIGN AND SETTING

In the Physical exercise during Adjuvant Chemotherapy Effectiveness Study (PACES) trial, 230 breast cancer patients receiving chemotherapy were randomized to supervised resistance and aerobic exercise (OnTrack), home-based physical activity (OncoMove) or usual care (UC). Data were reanalyzed as an adaptive trial using both Bayesian decision-theoretic and a frequentist group-sequential approach incorporating interim analyses after every 36 patients. Endpoint was chemotherapy treatment modifications (any vs. none). Bayesian analyses were performed for different continuation thresholds and settings with and without arm dropping and both in a 'pick-the-winner' and a 'pick-all-treatments-superior-to-control' setting.

RESULTS

Treatment modifications occurred in 34% of patients in UC and OncoMove vs. 12% in OnTrack (P = 0.002). Using a Bayesian-adaptive decision-theoretic design, OnTrack was identified as most effective after 72 patients in the 'pick-the-winner' setting and after 72-180 patients in the 'pick-all-treatments-superior-to-control' setting. In a frequentist setting, the trial would have been stopped after 180 patients, and the proportion of patients with treatment modifications was significantly lower for OnTrack than UC.

CONCLUSION

A Bayesian-adaptive decision-theoretic approach substantially reduced the sample size required for this three-arm exercise trial, especially in the 'pick-the-winner' setting.

Large Region of Homozygous (ROH) Identified in Indian Patients with Autosomal Recessive Limb-Girdle Muscular Dystrophy with p.Thr182Pro Variant in SGCB Gene

The sarcoglycanopathies are autosomal recessive limb-girdle muscular dystrophies (LGMDs) caused by the mutations in genes encoding the α, β, γ, and δ proteins which stabilizes the sarcolemma of muscle cells. The clinical phenotype is characterized by progressive proximal muscle weakness with childhood onset. Muscle biopsy findings are diagnostic in confirming dystrophic changes and deficiency of one or more sarcoglycan proteins. In this study, we summarized 1,046 LGMD patients for which a precise diagnosis was identified using targeted sequencing. The most frequent phenotypes identified in the patients are LGMDR1 (19.7%), LGMDR4 (19.0%), LGMDR2 (17.5%), and MMD1 (14.5%). Among the reported genes, each of CAPN3, SGCB, and DYSF variants was reported in more than 10% of our study cohort. The most common variant SGCB p.Thr182Pro was identified in 146 (12.5%) of the LGMD patients, and in 97.9% of these patients, the variant was found to be homozygous. To understand the genetic structure of the patients carrying SGCB p.Thr182Pro, we genotyped 68 LGMD patients using a whole genome microarray. Analysis of the array data identified a large ~1 Mb region of homozygosity (ROH) (chr4:51817441-528499552) suggestive of a shared genomic region overlapping the recurrent missense variant and shared across all 68 patients. Haplotype analysis identified 133 marker haplotypes that were present in ~85.3% of the probands as a double allele and absent in all random controls. We also identified 5 markers (rs1910739, rs6852236, rs13122418, rs13353646, and rs6554360) which were present in a significantly higher proportion in the patients compared to random control set ( $n=128$ ) and the population database. Of note, admixture analysis was suggestive of greater proportion of West Eurasian/European ancestry as compared to random controls. Haplotype analysis and frequency in the population database indicate a probable event of founder effect. Further systematic study is needed to identify the communities and regions where the SGCB p.Thr182Pro variant is observed in higher proportions. After identifying these communities and//or region, a screening program is needed to identify carriers and provide them counselling.

Somatic yolk sac differentiation in tumors of the gynecologic tract: A report of two cases and review of the literature

•Somatic yolk sac tumor differentiation associated with malignant neoplasms is uncommon and associated with poor outcome.•In the gynecologic tract, somatic yolk sac differentiation most often arises in postmenopausal patients.•Somatic yolk sac differentiation shares driver mutations with and likely differentiates from the corresponding carcinoma.•This is the first report of somatic yolk sac differentiation in the gynecologic tract from a non-epithelial malignancy.

k-Space Hyperspectral Imaging by a Birefringent Common-Path Interferometer

Fourier-plane microscopy is a powerful tool for measuring the angular optical response of a plethora of materials and photonic devices. Among them, optical microcavities feature distinctive energy-momentum dispersions, crucial for a broad range of fundamental studies and applications. However, measuring the whole momentum space (k-space) with sufficient spectral resolution using standard spectroscopic techniques is challenging, requiring long and alignment-sensitive scans. Here, we introduce a k-space hyperspectral microscope, which uses a common-path birefringent interferometer to image photoluminescent organic microcavities, obtaining an angle- and wavelength-resolved view of the samples in only one measurement. The exceptional combination of angular and spectral resolution of our technique allows us to reconstruct a three-dimensional (3D) map of the cavity dispersion in the energy-momentum space, revealing the polarization-dependent behavior of the resonant cavity modes. Furthermore, we apply our technique for the characterization of a dielectric nanodisk metasurface, evidencing the angular and spectral behavior of its anapole mode. This approach is able to provide a complete optical characterization for materials and devices with nontrivial angle-/wavelength-dependent properties, fundamental for future developments in the fields of topological photonics and optical metamaterials.

On the robustness of machine learning algorithms toward microfluidic distortions for cell classification via on-chip fluorescence microscopy

Single-cell imaging and sorting are critical technologies in biology and clinical applications. The power of these technologies is increased when combined with microfluidics, fluorescence markers, and machine learning. However, this quest faces several challenges. One of these is the effect of the sample flow velocity on the classification performances. Indeed, cell flow speed affects the quality of image acquisition by increasing motion blur and decreasing the number of acquired frames per sample. We investigate how these visual distortions impact the final classification task in a real-world use-case of cancer cell screening, using a microfluidic platform in combination with light sheet fluorescence microscopy. We demonstrate, by analyzing both simulated and experimental data, that it is possible to achieve high flow speed and high accuracy in single-cell classification. We prove that it is possible to overcome the 3D slice variability of the acquired 3D volumes, by relying on their 2D sum z-projection transformation, to reach an efficient real time classification with an accuracy of 99.4% using a convolutional neural network with transfer learning from simulated data. Beyond this specific use-case, we provide a web platform to generate a synthetic dataset and to investigate the effect of flow speed on cell classification for any biological samples and a large variety of fluorescence microscopes (https://www.creatis.insa-lyon.fr/site7/en/MicroVIP).

Integrated optical device for Structured Illumination Microscopy

Structured Illumination Microscopy (SIM) is a key technology for high resolution and super-resolution imaging of biological cells and molecules. The spread of portable and easy-to-align SIM systems requires the development of novel methods to generate a light pattern and to shift it across the field of view of the microscope. Here we show a miniaturized chip that incorporates optical waveguides, splitters, and phase shifters, to generate a 2D structured illumination pattern suitable for SIM microscopy. The chip creates three point-sources, coherent and controlled in phase, without the need for further alignment. Placed in the pupil of a microscope's objective, the three sources generate a hexagonal illumination pattern on the sample, which is spatially translated thanks to thermal phase shifters. We validate and use the chip, upgrading a commercial inverted fluorescence microscope to a SIM setup and we image biological sample slides, extending the resolution of the microscope.

Cognitive Reserve Modulates Brain Structure and Cortical Architecture in the Alzheimer's Disease

BACKGROUND

Cognitive reserve (CR) explains the individual resilience to neurodegeneration.

OBJECTIVE

The present study investigated the effect of CR in modulating brain cortical architecture.

METHODS

278 individuals [110 Alzheimer's disease (AD), 104 amnestic mild cognitive impairment (aMCI) due to AD, 64 healthy subjects (HS)] underwent a neuropsychological evaluation and 3T-MRI. Cortical thickness (CTh) and fractal dimension (FD) were assessed. Years of formal education were used as an index of CR by which participants were divided into high and low CR (HCR and LCR). Within-group differences in cortical architecture were assessed as a function of CR. Associations between cognitive scores and cortical measures were also evaluated.

RESULTS

aMCI-HCR compared to aMCI-LCR patients showed significant decrease of CTh in the right temporal and in the left prefrontal lobe. Moreover, they showed increased FD in the right temporal and in the left temporo-parietal lobes. Patients with AD-HCR showed reduced CTh in several brain areas and reduced FD in the left temporal cortices when compared with AD-LCR subjects. HS-HCR showed a significant increase of CTh in prefrontal areas bilaterally, and in the right parieto-occipital cortices. Finally, aMCI-HCR showed significant positive associations between brain measures and memory and executive performance.

CONCLUSION

CR modulates the cortical architecture at pre-dementia stage only. Indeed, only patients with aMCI showed both atrophy (likely due to neurodegeneration) alongside richer brain folding (likely due to reserve mechanisms) in temporo-parietal areas. This opposite trend was not observed in AD and HS. Our data confirm the existence of a limited time-window for CR modulation at the aMCI stage.