Illumination and fluorescence collection volumes for fiber optic probes in tissue

Targeted micro-fiber arrays for measuring and manipulating localized multi-scale neural dynamics over large, deep brain volumes during behavior

Neural population dynamics relevant to behavior vary over multiple spatial and temporal scales across three-dimensional volumes. Current optical approaches lack the spatial coverage and resolution necessary to measure and manipulate naturally occurring patterns of large-scale, distributed dynamics within and across deep brain regions such as the striatum. We designed a new micro-fiber array approach capable of chronically measuring and optogenetically manipulating local dynamics across over 100 targeted locations simultaneously in head-fixed and freely moving mice, enabling the investigation of cell-type- and neurotransmitter-specific signals over arbitrary 3D volumes at a spatial resolution and coverage previously inaccessible. We applied this method to resolve rapid dopamine release dynamics across the striatum, revealing distinct, modality-specific spatiotemporal patterns in response to salient sensory stimuli extending over millimeters of tissue. Targeted optogenetics enabled flexible control of neural signaling on multiple spatial scales, better matching endogenous signaling patterns, and the spatial localization of behavioral function across large circuits.

Plug-and-play fiber-optic sensors based on engineered cells for neurochemical monitoring at high specificity in freely moving animals

In vivo detection of neurochemicals, including neurotransmitters and neuromodulators, is critical for both understanding brain mechanisms and diagnosing brain diseases. However, few sensors are competent in monitoring neurochemical dynamics in vivo at high specificity. Here, we propose the fiber-optic probes based on engineered cells (FOPECs) for plug-and-play, real-time detection of neurochemicals in freely moving animals. Taking advantages of life-evolved neurochemical receptors as key components, the chemical specificity of FOPECs is unprecedented. We demonstrate the applications of FOPECs in real-time monitoring of neurochemical dynamics under various physiology and pathology conditions. With no requirement of viral infection in advance and no dependence on animal species, FOPECs can be widely adopted in vertebrates, such as mice, rats, rabbits, and chickens. Moreover, FOPECs can be used to monitor drug metabolisms in vivo. We demonstrated the neurochemical monitoring in blood circulation systems in vivo. We expect that FOPECs will benefit not only neuroscience study but also drug discovery.

Influence of the anatomical features of different brain regions on the spatial localization of fiber photometry signals

Fiber photometry is widely used in neuroscience labs for in vivo detection of functional fluorescence from optical indicators of neuronal activity with a simple optical fiber. The fiber is commonly placed next to the region of interest to both excite and collect the fluorescence signal. However, the path of both excitation and fluorescence photons is altered by the uneven optical properties of the brain, due to local variation of the refractive index, different cellular types, densities and shapes. Nonetheless, the effect of the local anatomy on the actual shape and extent of the volume of tissue that interfaces with the fiber has received little attention so far. To fill this gap, we measured the size and shape of fiber photometry efficiency field in the primary motor and somatosensory cortex, in the hippocampus and in the striatum of the mouse brain, highlighting how their substructures determine the detected signal and the depth at which photons can be mined. Importantly, we show that the information on the spatial expression of the fluorescent probes alone is not sufficient to account for the contribution of local subregions to the overall collected signal, and it must be combined with the optical properties of the tissue adjacent to the fiber tip.

A novel optical biosensor for in situ and small-scale monitoring of bacterial transport in saturated columns

In situ monitoring techniques can provide new insight into bacterial transport after inoculating exogenous bacteria into contaminated soils for bioremediation. A real-time and non-destructive optical sensor (the optrode) was employed to monitor in situ transport of two fluorescently labelled bacteria - Green Fluorescent Protein (Gfp)-labelled, hydrophilic Pseudomonas putida and Tomato Fluorescent Protein (td)-labelled, hydrophobic Rhodococcus erythropolis, in a saturated sand column with and without rhamnolipid surfactant. In situ measurements were made at three sampling ports in the column with the optrode in two sets of column experiments. In Experiment 1, liquid samples were extracted for ex situ analyses (plate counts and fluorescence), while in Experiment 2 no liquid samples were extracted. Extracting liquid samples for ex situ analyses in Experiment 1 disturbed in situ measurements; in situ measured bacterial concentrations were lower, or a significant lag in breakthrough occurred relative to ex situ measurements. In Experiment 2, the optrode worked well in monitoring bacterial transport, which gave consistent transport parameters at each sampling port. Moreover, the optrode enabled the impact of bacterial hydrophobicity and rhamnolipid surfactant on bacterial transport to be observed. Specifically, hydrophilic P. putida was transported faster through the column than hydrophobic R. erythropolis; we infer from this result that fewer P. putida cells adsorb to sand particles than do R. erythropolis cells. The rhamnolipid surfactant enhanced the transport of both hydrophilic and hydrophobic bacteria. These two observations are consistent with Lifshitz-van der Waals forces and acid-base interactions between bacteria and sand.

Comparative study of autofluorescence in flat and tapered optical fibers towards application in depth-resolved fluorescence lifetime photometry in brain tissue

As the scientific community seeks efficient optical neural interfaces with sub-cortical structures of the mouse brain, a wide set of technologies and methods is being developed to monitor cellular events through fluorescence signals generated by genetically encoded molecules. Among these technologies, tapered optical fibers (TFs) take advantage of the modal properties of narrowing waveguides to enable both depth-resolved and wide-volume light collection from scattering tissue, with minimized invasiveness with respect to standard flat fiber stubs (FFs). However, light guided in patch cords as well as in FFs and TFs can result in autofluorescence (AF) signal, which can act as a source of time-variable noise and limit their application to probe fluorescence lifetime in vivo. In this work, we compare the AF signal of FFs and TFs, highlighting the influence of the cladding composition on AF generation. We show that the autofluorescence signal generated in TFs has a peculiar coupling pattern with guided modes, and that far-field detection can be exploited to separate functional fluorescence from AF. On these bases, we provide evidence that TFs can be employed to implement depth-resolved fluorescence lifetime photometry, potentially enabling the extraction of a new set of information from deep brain regions, as time-correlating single photon counting starts to be applied in freely-moving animals to monitor the intracellular biochemical state of neurons.

Depth-resolved fiber photometry with a single tapered optical fiber implant

Fiber photometry is increasingly utilized to monitor fluorescent sensors of neural activity in the brain. However, most implementations are based on flat-cleaved optical fibers that can only interface with shallow tissue volumes adjacent to the fiber. We exploit modal properties of tapered optical fibers (TFs) to enable light collection over an extent of up to 2 mm of tissue and multisite photometry along the taper. Using a single TF, we simultaneously observed distinct dopamine transients in dorsal and ventral striatum in freely moving mice performing a simple, operant conditioning task. Collection volumes from TFs can also be engineered in both shape and size by microstructuring the nonplanar surface of the taper, to optically target multiple sites not only in the deep brain but, in general, in any biological system or organ in which light collection is beneficial but challenging because of light scattering and absorption.

Near real-time enumeration of live and dead bacteria using a fibre-based spectroscopic device

A rapid, cost-effective and easy method that allows on-site determination of the concentration of live and dead bacterial cells using a fibre-based spectroscopic device (the optrode system) is proposed and demonstrated. Identification of live and dead bacteria was achieved by using the commercially available dyes SYTO 9 and propidium iodide, and fluorescence spectra were measured by the optrode. Three spectral processing methods were evaluated for their effectiveness in predicting the original bacterial concentration in the samples: principal components regression (PCR), partial least squares regression (PLSR) and support vector regression (SVR). Without any sample pre-concentration, PCR achieved the most reliable results. It was able to quantify live bacteria from 108 down to 106.2 bacteria/mL and showed the potential to detect as low as 105.7 bacteria/mL. Meanwhile, enumeration of dead bacteria using PCR was achieved between 108 and 107 bacteria/mL. The general procedures described in this article can be applied or modified for the enumeration of bacteria within populations stained with fluorescent dyes. The optrode is a promising device for the enumeration of live and dead bacterial populations particularly where rapid, on-site measurement and analysis is required.

The Three-Dimensional Signal Collection Field for Fiber Photometry in Brain Tissue

Fiber photometry is used to monitor signals from fluorescent indicators in genetically-defined neural populations in behaving animals. Recently, fiber photometry has rapidly expanded and it now provides researchers with increasingly powerful means to record neural dynamics and neuromodulatory action. However, it is not clear how to select the optimal fiber optic given the constraints and goals of a particular experiment. Here, using combined confocal/2-photon microscope, we quantitatively characterize the fluorescence collection properties of various optical fibers in brain tissue. We show that the fiber size plays a major role in defining the volume of the optically sampled brain region, whereas numerical aperture impacts the total amount of collected signal and, marginally, the shape and size of the collection volume. We show that ~80% of the effective signal arises from 105 to 106 μm3 volume extending ~200 μm from the fiber facet for 200 μm core optical fibers. Together with analytical and ray tracing collection maps, our results reveal the light collection properties of different optical fibers in brain tissue, allowing for an accurate selection of the fibers for photometry and helping for a more precise interpretation of measurements in terms of sampled volume.

Open-source, cost-effective system for low-light in vivo fiber photometry

Fiber photometry uses genetically encoded optical reporters to link specific cellular activity in stereotaxically targeted brain structures to specific behaviors. There are still a number of barriers that have hindered the widespread adoption of this approach. This includes cost, but also the high-levels of light required to excite the fluorophore, limiting commercial systems to the investigation of short-term transients in neuronal activity to avoid damage of tissue by light. Here, we present a cost-effective optoelectronic system for in vivo fiber photometry that achieves high-sensitivity to changes in fluorescence intensity, enabling detection of optical transients of a popular calcium reporter with excitation powers as low as 100 nW. By realizing a coherent detection scheme and by using a photomultiplier tube as a detector, the system demonstrates reliable study of in vivo neuronal activity, positioning it for future use in the experiments inquiring into learning and memory processes. The system was applied to study stress-evoked calcium transients in corticotropin-releasing hormone neurons in the mouse hypothalamus.

Characterisation of a fibre optic Raman probe within a hypodermic needle

We demonstrate the first use of a multifibre Raman probe that fits inside the bore of a hypodermic needle. A Raman probe containing multiple collection fibres provides improved signal collection efficiency in biological samples compared with a previous two-fibre design. Furthermore, probe performance (signal-to-noise ratios) compared favourably with the performance achieved in previous Raman microscope experiments able to distinguish between benign lymph nodes, primary malignancies in lymph nodes and secondary malignancies in lymph nodes. The experimental measurements presented here give an indication of the sampling volume of the Raman needle probe in lymphoid tissues. Liquid tissue phantoms were used that contained scattering medium encompassing a range of scattering properties similar to those of a variety of tissue types, including lymph node tissues. To validate the appropriateness of the phantoms, the sampling depth of the probe was also measured in excised lymph node tissue. More than 50 % of Raman photons collected were found to originate from between the tip of the needle and a depth of 500 μm into the tissue. The needle probe presented here achieves spectral quality comparable to that in numerous studies previously demonstrating Raman disease discrimination. It is expected that this approach could achieve targeted subcutaneous tissue measurements and be viable for use for the in vivo Raman diagnostics of solid organs located within a few centimetres below the skin's surface. Graphical Abstract Schematic of multi-fibre Raman needle probe with disposible tips and proximal optical filtration.

Optrodes for combined optogenetics and electrophysiology in live animals

Optical tissue properties limit visible light depth penetration in tissue. Because of this, the recent development of optogenetic tools was quickly followed by the development of light delivery devices for in vivo optogenetics applications. We summarize the efforts made in the last decade to design neural probes that combine conventional electrophysiological recordings and optical channel(s) for optogenetic activation, often referred to as optodes or optrodes. Several aspects including challenges for light delivery in living brain tissue, the combination of light delivery with electrophysiological recordings, probe designs, multimodality, wireless implantable system, and practical considerations guiding the choice of configuration depending on the questions one seeks to address are presented.

Total viable bacterial count using a real time all-fibre spectroscopic system

Rapid, accurate and sensitive enumeration of bacterial populations in the natural environment is an essential task for many research fields. Widely used standard methods for counting bacteria such as heterotrophic plate count require 1 to 8 days of incubation time for limited accuracy, while more accurate and rapid techniques are often expensive and may require bulky equipment. In the present study, we have developed a computerized optical prototype for bacterial detection. The goal of this research was to estimate the potential of this optical system for Total Viable Bacterial Count in water. For this purpose, we tested water batches with different microbiological content. Bacterial detection was based on fluorescence enhanced by nucleic acid staining. High sensitivity was achieved by a stable diode pumped solid state laser, sensitive CCD spectrometer and in situ excitation and signal collection. The results have shown that the bacterial count from different water origins using our optical setup along with multivariate analysis presents a higher accuracy and a shorter detection time compared to standard methods. For example, in a case where the fluorescence signal is calibrated to the water batch regression line, the relative standard deviation of the optical system enumeration varies between 21 and 36%, while that of the heterotropic plate count counterpart varies between 41 and 59%. In summary, we conclude that the all-fibre optical system may offer the following advantages over conventional methods: near real time examinations, portability, sensitivity, accuracy and ability to detect 10(2) to 10(8) CFU per ml bacterial concentrations.

Novel fiber optic detection method for in situ analysis of fluorescently labeled biosensor organisms

This research presents a novel, time-resolved fiber-optic "Optrode" system for accurate real-time in situ detection of fluorescent proteins produced by biosensor organisms. The Optrode fluorescence detection system was able to identify, characterize, differentiate, and quantify red and green fluorescently labeled organisms, individually and in mixed aqueous cultures. Detection was also possible in sand systems, where a consistent reduction in signal intensity indicates that signal collection volume was reduced by one-third. The optrode was shown to be sensitive enough to detect fluorescently labeled cell concentrations of 1.9 × 10(4) CFU/mL, indicating it is suitable for detecting typical concentrations of degrader organisms reported in bioremediation trials. The effect of fluorophore photobleaching was characterized for different fluorescent proteins and demonstrated a linear relationship to cell concentration, meaning the effect can be accounted for within methods of fluorescence collection and analysis. Proof of concept is provided for all aspects of this research, which represents an important step toward the goal of achieving a complete, nondestructive, in situ monitoring system to characterize all aspects of microbial activity and gene expression.

A new optrode design for intramural optical recordings

Intramural measurements of V(m) and Ca(i)(2+) are important in the studies of cardiac arrhythmias and defibrillation. We developed a new design of an "optrode" (bundle of optical fibers) for use in intramural cardiac mapping. The optrodes are made from seven optical fibers with the fiber ends polished at 45° angle and coated with mirror surfaces. The optrodes are enclosed in smooth epoxy resin cast, which protects mirror surfaces from damage and ensures constant optrode diameter along its length. The optrodes are strong enough to be easily inserted into heart muscle, can be reused multiple times, and they may reduce artifacts in the measurements of the effects of defibrillation shocks on V(m).