A tilted fiber Bragg grating (TFBG) was integrated as the dispersive element in a high performance biomedical imaging system. The spectrum emitted by the 23 mm long active region of the fiber is projected through custom designed optics consisting of a cylindrical lens for vertical beam collimation and successively by an achromatic doublet onto a linear detector array. High resolution tomograms of biomedical samples were successfully acquired by the frequency domain OCT-system. Tomograms of ophthalmic and dermal samples obtained by the frequency domain OCT-system were obtained achieving 2.84 μm axial and 10.2 μm lateral resolution. The miniaturization reduces costs and has the potential to further extend the field of application for OCT-systems in biology, medicine and technology.
Nowadays, biophotonics is widely used in neuroscience. The effectiveness of biophotonic techniques, such as fluorescence imaging and optogenetics, is affected by the optical properties of the examined tissue. Therefore, knowledge of these properties is essential to carefully plan experiments. Mice and rats are widely used in neuroscience studies. However, reports about optical properties of their brains are very rare. We measured optical absorption μa and reduced scattering μ’s coefficients of native rat brain in the visible and near-infrared wavelength region, using contact spatially resolved spectroscopy (SRS). In this study, we estimate μa and μ’s for the rat cortex and discuss their stability in time. Additionally, variations in optical properties within and between samples were characterized. The results extend the range of known optical properties for the rat cortex, especially in the visible range, relevant to optogenetics. μa and μ’s are stable within a time span of four hours, and show low variation in and between brain samples. This indicates that a suitable protocol was used to estimate optical properties of rodent brain tissue. Since contact SRS is a non-destructive method, this technique could be used also to measure μa and μ’s in living animals. Moreover, the probe has small dimensions, allowing the characterization of optical properties in different structures of the brain.
Closed-loop brain computer interfaces are rapidly progressing due to their applications in fundamental neuroscience and prosthetics. For optogenetic experiments, the integration of optical stimulation and electrophysiological recordings is emerging as an imperative engineering research topic. Optical stimulation does not only bring the advantage of cell-type selectivity, but also provides an alternative solution to the electrical stimulation-induced artifacts, a challenge in closedloop architectures. A closed-loop system must identify the neuronal signals in real-time such that a strategy is selected immediately (within a few milliseconds) for delivering stimulation patterns. Real-time spike sorting poses important challenges especially when a large number of recording channels are involved. Here we present a prototype allowing simultaneous optical stimulation and electro-physiological recordings in a closed-loop manner. The prototype was implemented with online spike detection and classification capabilities for selective cell stimulation. Real-time spike sorting was achieved by computations with a high speed, low cost graphic processing unit (GPU). We have successfully demonstrated the closed-loop operation, i.e. optical stimulation in vivo based on spike detection from 8 tetrodes (32 channels). The performance of GPU computation in spike sorting for different channel numbers and signal lengths was also investigated.
A compact, fiber-based spectrometer for biomedical application utilizing a tilted fiber Bragg grating (TFBG) as
integrated dispersive element is demonstrated. Based on a 45° UV-written PS750 TFBG a refractive spectrometer with
2.06 radiant/μm dispersion and a numerical aperture of 0.1 was set up and tested as integrated detector for an optical
coherence tomography (OCT) system. Featuring a 23 mm long active region at the fiber the spectrum is projected via a
cylindrical lens for vertical beam collimation and focused by an achromatic doublet onto the detector array. Covering
740 nm to 860 nm the spectrometer was optically connected to a broadband white light interferometer and a wide field
scan head and electronically to an acquisition and control computer. Tomograms of ophthalmic and dermal samples
obtained by the frequency domain OCT-system were obtained achieving 2.84 μm axial and 7.6 μm lateral resolution.
Accurate knowledge of the optical properties of turbid media in the light path is important in NIR absorption
spectroscopy of biological tissues where multiple scattering complexes the collected light signals due to the non-uniform
tissue architecture. Several approaches such as time resolved spectroscopy and spatially resolved spectroscopy have been
proposed to measure the bulk optical properties of turbid media. Among them, double integrating sphere (DIS)
measurements are recognized as the "golden standard" for in vitro optical properties measurement of turbid media
because of its high accuracy and robustness in different conditions. A DIS system is convenient to measure the in vitro
optical properties of turbid media like intralipid solutions and biological tissues, since it measures the diffuse reflectance
and transmittance simultaneously. However, DIS measurements have been mostly limited to the optical window region
(400-1000 nm) or suffered from low signal levels on the detectors due to the absorption by water in the NIR region. In
this study, we developed a DIS system for optical property measurement in the 1300-2350 nm region based on a novel
wavelength tunable spectroscopic setup which incorporates a high power broadband supercontinuum laser and a high
precision monochromator. With this system, optical properties of intralipid solutions were measured in the wavelength
region of 1300-2350nm.
Standard FD-OCT systems suffer from a limited useful depth range due to the inherent complex conjugate artifacts and
continuous fall-off in sensitivity with distance from the zero delay. The techniques of dispersion encoded full range
(DEFR) frequency-domain optical coherence tomography (FD-OCT) and its enhanced version fast DEFR use the
dispersion mismatch between sample and reference arm to double the imaging depth range by iteratively suppressing
complex conjugate artifacts. Previously the computational complexity of DEFR prevented its application to fields where
real-time visualization or large volumetric datasets are needed. A graphics processing unit (GPU) with hundreds of
processing cores provides highly parallel computation capability to FD-OCT in which processing for each A-line is
identical and independent. In this paper, we adopted GPUs to accelerate DEFR, thereby significantly improving
reconstruction speed by a factor of >90 in respect to CPU based processing. A maximum display line rate of ~21 k-lines/
s for 2048 points/A-line using 10 iterations of the fast DEFR algorithm has been successively achieved, thereby
enabling the application of DEFR in fields where real time visualization is required. By comparison in the conjugate
artifact suppressed cross-sectional image of a mouse eye, there is no significant qualitative difference between the
corresponding CPU- and GPU-processed images.
KEYWORDS: Optical coherence tomography, Signal detection, Mirrors, Retinal scanning, In vivo imaging, Reconstruction algorithms, Microscopes, Spectroscopy, Imaging systems, Signal processing
The dispersion mismatch between sample and reference arm in frequency-domain OCT can be used to iteratively
suppress complex conjugate artifacts and thereby increase the imaging range. We propose a fast dispersion
encoded full range (DEFR) algorithm that detects multiple signal components per iteration. The influence of
different dispersion levels on the reconstruction quality is analyzed for in vivo retinal tomograms at 800 nm. Best
results have been achieved with about 30 mm SF11, with neglectable resolution decrease due to finite resolution
of the spectrometer. Our fast DEFR algorithm achieves an average suppression ratio of 55 dB and converges
within 5 to 10 iterations. The processing time on non-dedicated hardware was 5 to 10 seconds for tomograms
with 512 depth scans and 4096 sampling points per depth scan. Application of DEFR to the more challenging
1060 nm wavelength region is demonstrated by introducing an additional optical fibre in the sample arm.
We report a high-speed, dispersion-encoded, full-range (DEFR) swept-source optical coherence tomography system for in vivo ocular imaging and biometry of small animals. The fast DEFR algorithm removes the depth ambiguity, gives access to objects located at the zero delay position, and doubles the sampling depth to 2×5.0 mm (at −101 to −71 dB sensitivity) in a single scan using 2048 samples/depth scan 0.43 nm line width of a light source operating at 1056 nm with 70 nm tuning range. The acquisition speed (frames of 512 depth scans in 18.3 ms) permits precise on-line monitoring during positioning and provides cross-sectional views of the mouse eye. Preliminary studies demonstrate high-throughput, reproducible assessment of multiple biometric features (e.g., day-to-day reproducibility of axial length measurement ±5.3 µm) that is insensitive to eye motion sufficient for long-term monitoring.
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