Extended depth-of-field microscopy with a high-speed deformable mirror.

We present a wide-field fluorescence microscopy add-on that provides a fast, light-efficient extended depth-of-field (EDOF) using a deformable mirror with an update rate of 20 kHz. Out-of-focus contributions in the raw EDOF images are suppressed with a deconvolution algorithm derived directly from the microscope 3D optical transfer function. Demonstrations of the benefits of EDOF microscopy are shown with GCaMP-labeled mouse brain tissue.

Dual fluorescence-absorption deconvolution applied to extended-depth-of-field microscopy.

Fast imaging over large volumes can be obtained in a simple manner with extended-depth-of-field (EDOF) microscopy. A standard technique of Wiener deconvolution can correct for the blurring inherent in EDOF images. We compare Wiener deconvolution with an alternative, parameter-free technique based on the dual reconstruction of fluorescence and absorption layers in a sample. This alternative technique provides significantly enhanced reconstruction contrast owing to a quadratic positivity constraint that intrinsically favors sparse solutions. We demonstrate the advantages of this technique with mouse neuronal images acquired in vivo.

Population-scale three-dimensional reconstruction and quantitative profiling of microglia arbors.

MOTIVATION: The arbor morphologies of brain microglia are important indicators of cell activation. This article fills the need for accurate, robust, adaptive and scalable methods for reconstructing 3-D microglial arbors and quantitatively mapping microglia activation states over extended brain tissue regions. RESULTS: Thick rat brain sections (100-300 µm) were multiplex immunolabeled for IBA1 and Hoechst, and imaged by step-and-image confocal microscopy with automated 3-D image mosaicing, producing seamless images of extended brain regions (e.g. 5903 × 9874 × 229 voxels). An over-complete dictionary-based model was learned for the image-specific local structure of microglial processes. The microglial arbors were reconstructed seamlessly using an automated and scalable algorithm that exploits microglia-specific constraints. This method detected 80.1 and 92.8% more centered arbor points, and 53.5 and 55.5% fewer spurious points than existing vesselness and LoG-based methods, respectively, and the traces were 13.1 and 15.5% more accurate based on the DIADEM metric. The arbor morphologies were quantified using Scorcioni's L-measure. Coifman's harmonic co-clustering revealed four morphologically distinct classes that concord with known microglia activation patterns. This enabled us to map spatial distributions of microglial activation and cell abundances. AVAILABILITY AND IMPLEMENTATION: Experimental protocols, sample datasets, scalable open-source multi-threaded software implementation (C++, MATLAB) in the electronic supplement, and website (www.farsight-toolkit.org). http://www.farsight-toolkit.org/wiki/Population-scale_Three-dimensional_Reconstruction_and_Quanti-tative_Profiling_of_Microglia_Arbors CONTACT: broysam@central.uh.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Long-termin vivomonitoring of gliotic sheathing of ultrathin entropic coated brain microprobes with fiber-based optical coherence tomography.

Objective.Microfabricated neuroprosthetic devices have made possible important observations on neuron activity; however, long-term high-fidelity recording performance of these devices has yet to be realized. Tissue-device interactions appear to be a primary source of lost recording performance. The current state of the art for visualizing the tissue response surrounding brain implants in animals is immunohistochemistry + confocal microscopy, which is mainly performed after sacrificing the animal. Monitoring the tissue response as it develops could reveal important features of the response which may inform improvements in electrode design.Approach.Optical coherence tomography (OCT), an imaging technique commonly used in ophthalmology, has already been adapted for imaging of brain tissue. Here, we use OCT to achieve real-time,in vivomonitoring of the tissue response surrounding chronically implanted neural devices. The employed tissue-response-provoking implants are coated with a plasma-deposited nanofilm, which has been demonstrated as a biocompatible and anti-inflammatory interface for indwelling devices. We evaluate the method by comparing the OCT results to traditional histology qualitatively and quantitatively.Main results.The differences in OCT signal across the implantation period between the plasma group and the control reveal that the plasma-type coating of otherwise rigid brain probes (glass) only slightly improve the glial encapsulation in the brain parenchyma indicating that geometrical or mechanical influences are dominating the encapsulation process.Significance.Our approach can long-term monitor and compare the tissue-response to chronically-implanted neural probes with and withour plasma coating in living animal models. Our findings provide valuable insigh to the well acknowledged yet not solved challenge.

The effect of acoustically-induced cavitation on the permeance of a bullfrog urinary bladder.

It is well known that ultrasound enhances drug delivery to tissues, although there is not a general consensus about the responsible mechanisms. However, it is known that the most important factor associated with ultrasonically-enhanced drug permeance through tissues is cavitation. Here we report results from research conducted using a experimental approach adapted from single bubble sonoluminescence experiments which generates very well defined acoustic fields and allows controlled activation and location of cavitation. The experimental design requires that a biological tissue be immersed inside a highly degassed liquid media to avoid random bubble nucleation. Therefore, live frog bladders were used as the living tissue due to their high resistance to hypoxia. Tissue membrane permeance was measured using radiolabeled urea. The results show that an increase in tissue permeance only occurs when cavitation is present near the tissue membrane. Moreover, confocal microscopy shows a direct correlation between permeance increases and physical damage to the tissue.

Release of nerve growth factor from HEMA hydrogel-coated substrates and its effect on the differentiation of neural cells.

Local pharmacological intervention may be needed to ensure the long-term performance of neural prosthetic devices because of insertion-related neuron loss and reactive cell responses that form compact sheaths, leading to decreased device performance. We propose that local delivery of neurotrophins would enhance neuron survival and promote neuron sprouting toward device electrodes, thus providing improved electrode-neuron communication and device performance for recording and stimulating CNS activity. In this study, three different types of poly(2-hydroxyethyl methacrylate) (pHEMA) hydrogels were developed and assessed for storage capacity and release rates of the neurotrophin, nerve growth factor (NGF). Additionally, a method was developed for routine coating of microfabricated neuroprosthetic devices with the different pHEMA hydrogels. Biological responses to hydrogel-delivered NGF from the devices were measured using primary cell cultures of dorsal root ganglion (DRG) neurons. Neuron process growth was used to assess biological responses to released NGF. When targeted media concentrations were the same, responses to bath-applied NGF and NGF released from pHEMA hydrogels were not significantly different. When NGF was released from lysine-conjugated pHEMA hydrogels, a significant increase in process growth was observed. Our studies demonstrate that pHEMA coatings can be used on neural devices consistent with the needs for local neurotrophin delivery in the brain.

Improved detection of branching points in algorithms for automated neuron tracing from 3D confocal images.

Automated tracing of neuronal processes from 3D confocal microscopy images is essential for quantitative neuroanatomy and neuronal assays. Two basic approaches are described in the literature-one based on skeletonization and another based on sequential tracing along neuronal processes. This article presents algorithms for improving the rate of detection, and the accuracy of estimating the location and process angles at branching points for the latter class of algorithms. The problem of simultaneously detecting branch points and estimating their measurements is formulated as a generalized likelihood ratio test defined on a spatial neighborhood of each candidate point, in which likelihoods were computed using a ridge detection approach. The average detection rate increased from from 37 to 86%. The average error in locating the branch points decreased from 2.6 to 2.1 voxels in 3D images. The generalized hypothesis test improves the rate of detection of branching points, and the accuracy of location estimates, enabling a more complete extraction of neuroanatomy and more accurate counting of branch points in neuronal assays. More accurate branch point morphometry is valuable for image registration and change analysis.

Associative image analysis: a method for automated quantification of 3D multi-parameter images of brain tissue.

Brain structural complexity has confounded prior efforts to extract quantitative image-based measurements. We present a systematic 'divide and conquer' methodology for analyzing three-dimensional (3D) multi-parameter images of brain tissue to delineate and classify key structures, and compute quantitative associations among them. To demonstrate the method, thick ( approximately 100 microm) slices of rat brain tissue were labeled using three to five fluorescent signals, and imaged using spectral confocal microscopy and unmixing algorithms. Automated 3D segmentation and tracing algorithms were used to delineate cell nuclei, vasculature, and cell processes. From these segmentations, a set of 23 intrinsic and 8 associative image-based measurements was computed for each cell. These features were used to classify astrocytes, microglia, neurons, and endothelial cells. Associations among cells and between cells and vasculature were computed and represented as graphical networks to enable further analysis. The automated results were validated using a graphical interface that permits investigator inspection and corrective editing of each cell in 3D. Nuclear counting accuracy was >89%, and cell classification accuracy ranged from 81 to 92% depending on cell type. We present a software system named FARSIGHT implementing our methodology. Its output is a detailed XML file containing measurements that may be used for diverse quantitative hypothesis-driven and exploratory studies of the central nervous system.

Cryopreservation of transfected primary dorsal root ganglia neurons.

Primary dorsal root ganglia (DRG) neurons are often used to investigate the relative strength of various guidance cues to promote re-growth in vitro. Current methods of neuron isolation are laborious and disposal of excess dissected cells is inefficient. Traditional immunostaining techniques are inadequate to visualize real-time neurite outgrowth in co-culture. Cryopreservation, in combination with transfection techniques, may provide a viable solution to both under-utilized tissue and insufficient methods of visualization. This study aims to qualitatively and quantitatively demonstrate successful cryopreservation of primary transfected and non-transfected DRG neurons. Fluorescent micrographs were used to assess morphology after 24h in culture and suggest similarities between freshly isolated neurons and neurons which have been transfected and/or cryopreserved. Quantitative measurements of neuron outgrowth (specifically, primary neurites, branch points and total neurite length) indicate that neuron outgrowth is not altered by cryopreservation. Transfected neurons have stunted outgrowth at 24h.

Modulation of cultured neural networks using neurotrophin release from hydrogel-coated microelectrode arrays.

Polyacrylamide and poly(ethylene glycol) diacrylate hydrogels were synthesized and characterized for use as drug release and substrates for neuron cell culture. Protein release kinetics was determined by incorporating bovine serum albumin (BSA) into hydrogels during polymerization. To determine if hydrogel incorporation and release affect bioactivity, alkaline phosphatase was incorporated into hydrogels and a released enzyme activity determined using the fluorescence-based ELF-97 assay. Hydrogels were then used to deliver a brain-derived neurotrophic factor (BDNF) from hydrogels polymerized over planar microelectrode arrays (MEAs). Primary hippocampal neurons were cultured on both control and neurotrophin-containing hydrogel-coated MEAs. The effect of released BDNF on neurite length and process arborization was investigated using automated image analysis. An increased spontaneous activity as a response to the released BDNF was recorded from the neurons cultured on the top of hydrogel layers. These results demonstrate that proteins of biological interest can be incorporated into hydrogels to modulate development and function of cultured neural networks. These results also set the stage for development of hydrogel-coated neural prosthetic devices for local delivery of various biologically active molecules.

High-throughput label-free flow cytometry based on matched-filter compressive imaging.

We present a fast label-free computational flow cytometer based on a strategy of compressive imaging. Scattered light from flowing objects is sub-divided into user-defined basis patterns by a deformable mirror and routed to different detectors associated with each pattern. The patterns can be optimized to be matched to the object features of interest, thus facilitating object identification and separation. Compared to conventional scanning flow cytometers, our technique provides increased information capacity without sacrificing flow velocity. Unique features of our matched-filter strategy are that it can simultaneously probe multiple objects throughout large fields of view with long depths of field. In our proof-of-concept demonstrations, we achieve throughputs of over 10,000 particles/s, working at flow velocities of over 1m/s.

Axial localization with modulated-illumination extended-depth-of-field microscopy.

High-speed volumetric imaging represents a challenge in microscopy applications. We demonstrate a technique for acquiring volumetric images based on the extended depth of field microscopy with a fast focal scan and modulated illumination. By combining two frames with different illumination ramps, we can perform local depth ranging of the sample at speeds of up to half the camera frame rate. Our technique is light efficient, provides diffraction-limited resolution, enables axial localization that is largely independent of sample size, and can be operated with any standard widefield microscope based on fluorescence or darkfield contrast as a simple add-on. We demonstrate the accuracy of axial localization and applications of the technique to various dynamic extended samples, including in-vivo mouse brain.

Reduced cell attachment to poly(2-hydroxyethyl methacrylate)-coated ventricular catheters in vitro.

The majority of patients with hydrocephalus are dependent on ventriculoperitoneal shunts for diversion of excess cerebrospinal fluid. Unfortunately, these shunts are failure-prone and over half of all life-threatening pediatric failures are caused by obstruction of the ventricular catheter by the brain's resident immune cells, reactive microglia and astrocytes. Poly(2-hydroxyethyl methacrylate) (PHEMA) hydrogels are widely used for biomedical implants. The extreme hydrophilicity of PHEMA confers resistance to protein fouling, making it a strong candidate coating for ventricular catheters. With the advent of initiated chemical vapor deposition (iCVD), a solvent-free coating technology that creates a polymer in thin film form on a substrate surface by introducing gaseous reactant species into a vacuum reactor, it is now possible to apply uniform polymer coatings on complex three-dimensional substrate surfaces. iCVD was utilized to coat commercially available ventricular catheters with PHEMA. The chemical structure was confirmed on catheter surfaces using Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy. PHEMA coating morphology was characterized by scanning electron microscopy. Testing PHEMA-coated catheters against uncoated clinical-grade catheters in an in vitro hydrocephalus catheter bioreactor containing co-cultured astrocytes and microglia revealed significant reductions in cell attachment to PHEMA-coated catheters at both 17-day and 6-week time points. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 106B: 1268-1279, 2018.

Directed cell growth on protein-functionalized hydrogel surfaces.

Biochemical surface modification has been used to direct cell attachment and growth on a biocompatible gel surface. Acrylamide-based hydrogels were photo-polymerized in the presence of an acroyl-streptavidin monomer to create planar, functionalized surfaces capable of binding biotin-labelled proteins. Soft protein lithography (microcontact printing) of proteins was used to transfer the biotinylated extracellular matrix proteins, fibronectin and laminin, and the laminin peptide biotin-IKVAV, onto modified surfaces. As a biological assay, we plated LRM55 astroglioma and primary rat hippocampal neurons on patterned hydrogels. We found both cell types to selectively adhere to areas patterned with biotin-conjugated proteins. Fluorescence and bright-field modes of microscopy were used to assess cell attachment and cell morphology on modified surfaces. LRM55 cells were found to attach to protein-stamped regions of the hydrogel only. Neurons exhibited significant neurite extension after 72h in vitro, and remained viable on protein-stamped areas for more than 4 weeks. Patterned neurons developed functionally active synapses, as measured by uptake of the dye FM1-43FX. Results from this study suggest that hydrogel surfaces can be patterned with multiple proteins to direct cell growth and attachment.

Low-density neuronal networks cultured using patterned poly-l-lysine on microelectrode arrays.

Synaptic activity recorded from low-density networks of cultured rat hippocampal neurons was monitored using microelectrode arrays (MEAs). Neuronal networks were patterned with poly-l-lysine (PLL) using microcontact printing (microCP). Polydimethysiloxane (PDMS) stamps were fabricated with relief structures resulting in patterns of 2 microm-wide lines for directing process growth and 20 microm-diameter circles for cell soma attachment. These circles were aligned to electrode sites. Different densities of neurons were plated in order to assess the minimal neuron density required for development of an active network. Spontaneous activity was observed at 10-14 days in networks using neuron densities as low as 200 cells/mm(2). Immunocytochemistry demonstrated the distribution of dendrites along the lines and the location of foci of the presynaptic protein, synaptophysin, on neuron somas and dendrites. Scanning electron microscopy demonstrated that single fluorescent tracks contained multiple processes. Evoked responses of selected portions of the networks were produced by stimulation of specific electrode sites. In addition, the neuronal excitability of the network was increased by the bath application of high K(+) (10-12 mM). Application of DNQX, an AMPA antagonist, blocked all spontaneous activity, suggesting that the activity is excitatory and mediated through glutamate receptors.

Complex impedance spectroscopy for monitoring tissue responses to inserted neural implants.

A series of animal experiments was conducted to characterize changes in the complex impedance of chronically implanted electrodes in neural tissue. Consistent trends in impedance changes were observed across all animals, characterized as a general increase in the measured impedance magnitude at 1 kHz. Impedance changes reach a peak approximately 7 days post-implant. Reactive responses around individual electrodes were described using immuno- and histo-chemistry and confocal microscopy. These observations were compared to measured impedance changes. Several features of impedance changes were able to differentiate between confined and extensive histological reactions. In general, impedance magnitude at 1 kHz was significantly increased in extensive reactions, starting about 4 days post-implant. Electrodes with extensive reactions also displayed impedance spectra with a characteristic change at high frequencies. This change was manifested in the formation of a semi-circular arc in the Nyquist space, suggestive of increased cellular density in close proximity to the electrode site. These results suggest that changes in impedance spectra are directly influenced by cellular distributions around implanted electrodes over time and that impedance measurements may provide an online assessment of cellular reactions to implanted devices.

Functionalized hydrogel surfaces for the patterning of multiple biomolecules.

Patterning of multiple proteins and enzymes onto biocompatible surfaces can provide multiple signals to control cell attachment and growth. Acrylamide-based hydrogels were photo-polymerized in the presence of streptavidin-acrylamide, resulting in planar gel surfaces functionalized with the streptavidin protein. This surface was capable of binding biotin-labeled biomolecules. The proteins fibronectin and laminin, the enzyme alkaline phosphatase, and the photo-protein R-phycoerythrin were patterned using soft lithographic techniques. Polydimethylsiloxane stamps were used to transfer biotinylated proteins onto streptavidin-conjugated hydrogel surfaces. Stamped biomolecules were spatially resolved to feature sizes of 10 mum. Fluorescence measurements were used to assess protein transfer and enzyme functionality on modified surfaces. Our results demonstrate that hydrogel surfaces can be patterned with multiple proteins and enzymes, with retention of biological and catalytic activity. These surfaces are biocompatible and provide cues for cell attachment and growth. (c) 2006 Wiley Periodicals, Inc. J Biomed Mater Res 2007.

Electrical stimulation-induced cell clustering in cultured neural networks.

Planar microelectrode arrays (MEAs) are widely used to record electrical activity from neural networks. However, only a small number of functional recording sites frequently show electrical activity. One contributing factor may be that neurons in vitro receive insufficient synaptic input to develop into fully functional networks. In this study, electrical stimulation was applied to neurons mimicking synaptic input. Various stimulation paradigms were examined. Stimulation amplitude and frequency were tailored to prevent cell death. Two effects of stimulation were observed when 3-week-old cultures were stimulated: (1) clusters of neural cells were observed adjacent to stimulating electrodes and (2) an increase in spontaneous neuronal activity was recorded at stimulating electrodes. Immunocytochemical analysis indicates that stimulation may cause both new neuron process growth as well as astrocyte activation. These data indicate that electrical stimulation can be used as a tool to modify neural networks at specific electrode sites and promote electrical activity.

BCI Meeting 2005--workshop on signals and recording methods.

This paper describes the highlights of presentations and discussions during the Third International BCI Meeting in a workshop that evaluated potential brain-computer interface (BCI) signals and currently available recording methods. It defined the main potential user populations and their needs, addressed the relative advantages and disadvantages of noninvasive and implanted (i.e., invasive) methodologies, considered ethical issues, and focused on the challenges involved in translating BCI systems from the laboratory to widespread clinical use. The workshop stressed the critical importance of developing useful applications that establish the practical value of BCI technology.

Toward a better understanding of the cellular basis for cerebrospinal fluid shunt obstruction: report on the construction of a bank of explanted hydrocephalus devices.

OBJECTIVE Shunt obstruction by cells and/or tissue is the most common cause of shunt failure. Ventricular catheter obstruction alone accounts for more than 50% of shunt failures in pediatric patients. The authors sought to systematically collect explanted ventricular catheters from the Seattle Children's Hospital with a focus on elucidating the cellular mechanisms underlying obstruction. METHODS In the operating room, explanted hardware was placed in 4% paraformaldehyde. Weekly, samples were transferred to buffer solution and stored at 4°C. After consent was obtained for their use, catheters were labeled using cell-specific markers for astrocytes (glial fibrillary acidic protein), microglia (ionized calcium-binding adapter molecule 1), and choroid plexus (transthyretin) in conjunction with a nuclear stain (Hoechst). Catheters were mounted in custom polycarbonate imaging chambers. Three-dimensional, multispectral, spinning-disk confocal microscopy was used to image catheter cerebrospinal fluid-intake holes (10× objective, 499.2-µm-thick z-stack, 2.4-µm step size, Olympus IX81 inverted microscope with motorized stage and charge-coupled device camera). Values are reported as the mean ± standard error of the mean and were compared using a 2-tailed Mann-Whitney U-test. Significance was defined at p < 0.05. RESULTS Thirty-six ventricular catheters have been imaged to date, resulting in the following observations: 1) Astrocytes and microglia are the dominant cell types bound directly to catheter surfaces; 2) cellular binding to catheters is ubiquitous even if no grossly visible tissue is apparent; and 3) immunohistochemical techniques are of limited utility when a catheter has been exposed to Bugbee wire electrocautery. Statistical analysis of 24 catheters was performed, after excluding 7 catheters exposed to Bugbee wire cautery, 3 that were poorly fixed, and 2 that demonstrated pronounced autofluorescence. This analysis revealed that catheters with a microglia-dominant cellular response tended to be implanted for shorter durations (24.7 ± 6.7 days) than those with an astrocyte-dominant response (1183 ± 642 days; p = 0.027). CONCLUSIONS Ventricular catheter occlusion remains a significant source of shunt morbidity in the pediatric population, and given their ability to intimately associate with catheter surfaces, astrocytes and microglia appear to be critical to this pathophysiology. Microglia tend to be the dominant cell type on catheters implanted for less than 2 months, while astrocytes tend to be the most prevalent cell type on catheters implanted for longer time courses and are noted to serve as an interface for the secondary attachment of ependymal cells and choroid plexus.