Neurophotonics thanks the individuals who served as reviewers in 2018.

Functional near-infrared spectroscopy (fNIRS) is a noninvasive functional imaging technique measuring hemodynamic changes including oxygenated (O₂Hb) and deoxygenated (HHb) hemoglobin. Low frequency (LF; 0.01 to 0.15 Hz) band is commonly analyzed in fNIRS to represent neuronal activation. However, systemic physiological artifacts (i.e., nonneuronal) likely occur also in overlapping frequency bands. We measured peripheral photoplethysmogram (PPG) signal concurrently with fNIRS (at prefrontal region) to extract the low-frequency oscillations (LFOs) as systemic noise regressors. We investigated three main points in this study: (1) the relationship between prefrontal fNIRS and peripheral PPG signals; (2) the denoising potential using these peripheral LFOs, and (3) the innovative ways to avoid the false-positive result in fNIRS studies. We employed spatial working memory (WM) and control tasks (e.g., resting state) to illustrate these points. Our results showed: (1) correlation between signals from prefrontal fNIRS and peripheral PPG is region-dependent. The high correlation with peripheral ear signal (i.e., O₂Hb) occurred mainly in frontopolar regions in both spatial WM and control tasks. This may indicate the finding of task-dependent effect even in peripheral signals. We also found that the PPG recording at the ear has a high correlation with prefrontal fNIRS signal than the finger signals. (2) The systemic noise was reduced by 25% to 34% on average across regions, with a maximum of 39% to 58% in the highly correlated frontopolar region, by using these peripheral LFOs as noise regressors. (3) By performing the control tasks, we confirmed that the statistically significant activation was observed in the spatial WM task, not in the controls. This suggested that systemic (and any other) noises unlikely violated the major statistical inference. (4) Lastly, by denoising using the task-related signals, the significant activation of region-of-interest was still observed suggesting the manifest task-evoked response in the spatial WM task.

Microscopy methods used to measure Förster resonance energy transfer (FRET) between fluorescently labeled proteins can provide information on protein interactions in cells. However, these methods are diffraction-limited, thus do not enable the resolution of the nanodomains in which such interactions occur in cells. To overcome this limitation, we assess FRET with an imaging system combining fluorescence lifetime imaging microscopy with stimulated emission depletion, termed fluorescence lifetime imaging nanoscopy (FLIN). The resulting FRET-FLIN approach utilizes immunolabeling of proteins in fixed cultured neurons. We demonstrate the capacity to discriminate nanoclusters of synaptic proteins exhibiting variable degrees of interactions with labeled binding partners inside dendritic spines of hippocampal neurons. This method enables the investigation of FRET within nanodomains of cells, approaching the scale of molecular signaling.

Large vessel occlusion (LVO) stroke might cause different degrees of hemodynamic impairment that affects microcirculation and contributes to metabolic derangement. Time-domain near-infrared spectroscopy (TD-NIRS) estimates the oxygenation of microcirculation of cerebral outer layers. We measure hemoglobin species and tissue oxygen saturation (StO₂) of anterior circulation stroke patients, classified as LVO or lacunar, and assess the differences compared with controls and according to LVO recanalization status. Fiducial markers categorize the brain region below each TD-NIRS probe as ischemic or nonstroke areas. The study includes 47 consecutive acute ischemic stroke patients and 35 controls. The ischemic area has significantly higher deoxy-hemoglobin (HbR) and total hemoglobin (HbT) compared with controls in both recanalized and nonrecanalized patients but lower StO₂ only in recanalized patients. Recanalized patients have significantly lower mean StO₂ in the ipsilateral hemisphere compared with nonrecanalized patients. This is the first study to report TD-NIRS measurements in acute ischemic stroke patients. TD-NIRS is able to detect significant differences in hemoglobin species in LVO stroke compared with controls and according to recanalization status. This preliminary data might suggest that StO₂ can serve as a surrogate functional marker of the metabolic activity of rescued brain tissue.

The transcranial photobiomodulation (t-PBM) technique is a promising approach for the treatment of a wide range of neuropsychiatric disorders, including disorders characterized by poor regulation of emotion such as major depressive disorder (MDD). We examine various approaches to deliver red and near-infrared light to the dorsolateral prefrontal cortex (dlPFC) and ventromedial prefrontal cortex (vmPFC) in the human brain, both of which have shown strong relevance to the treatment of MDD. We apply our hardware-accelerated Monte Carlo simulations to systematically investigate the light penetration profiles using a standard adult brain atlas. To better deliver light to these regions-of-interest, we study, in particular, intranasal and transcranial illumination approaches. We find that transcranial illumination at the F3–F4 location (based on 10–20 system) provides excellent light delivery to the dlPFC, while a light source located in close proximity to the cribriform plate is well-suited for reaching the vmPFC, despite the fact that accessing the latter location may require a minimally invasive approach. Alternative noninvasive illumination strategies for reaching vmPFC are also studied and both transcranial illumination at the Fp1–FpZ–Fp2 location and intranasal illumination in the mid-nose region are shown to be valid. Different illumination wavelengths, ranging from 670 to 1064 nm, are studied and the amounts of light energy deposited to a wide range of brain regions are quantitatively compared. We find that 810 nm provided the overall highest energy delivery to the targeted regions. Although our simulations carried out on locations and wavelengths are not designed to be exhaustive, the proposed illumination strategies inform the design of t-PBM systems likely to improve brain emotion regulation, both in clinical research and practice.

The goal of understanding the architecture of neural circuits at the synapse level with a brain-wide perspective has powered the interest in high-speed and large field-of-view volumetric imaging at subcellular resolution. Here, we developed a method combining tissue expansion and light-sheet fluorescence microscopy to allow extended volumetric super resolution high-speed imaging of large mouse brain samples. We demonstrate the capabilities of this method by performing two color fast volumetric super resolution imaging of mouse CA1 and dentate gyrus molecular-, granule cell-, and polymorphic layers. Our method enables an exact evaluation of granule cell and neurite morphology within the context of large cell ensembles spanning several orders of magnitude in resolution. We found that imaging a brain region of 1  mm³ in super resolution using light-sheet fluorescence expansion microscopy is about 17-fold faster than imaging the same region by a current state-of-the-art high-resolution confocal laser scanning microscope.

The soft cranial window using polydimethylsiloxane allows direct multiple access to neural tissue during long-term monitoring. However, the chronic effects of soft window installation on the brain have not been fully studied. Here, we investigate the long-term effects of soft window installation on sensory-evoked cerebral hemodynamics and neuronal activity. We monitored the brain tissue immunocytohistology for 6 weeks postinstallation. Heightened reactive astrocytic and microglia levels were found at 2 weeks postinstallation. By 6 weeks postinstallation, mice had expression levels similar to those of normal animals. We recorded sensory-evoked hemodynamics of the barrel cortex and LFP during whisker stimulation at these time points. Animals at 6 weeks postinstallation showed stronger hemodynamic responses and focalized barrel mapping than 2-week postoperative mice. LFP recordings of 6-week postoperative mice also showed higher neural activity at the barrel column corresponding to the stimulated whisker. Furthermore, the expression level of interleukin-1β was highly upregulated at 2 weeks postinstallation. When we treated animals postoperatively with minocycline plus N-acetylcystein, a drug-suppressing inflammatory cytokine, these animals did not show declined hemodynamic responses and neuronal activities. This result suggests that neuroinflammation following soft window installation may alter hemodynamic and neuronal responses upon sensory stimulation.

Optogenetics has revolutionized the study of circuit function in the brain, by allowing activation of specific ensembles of neurons by light. However, this technique has not yet been exploited extensively at the subcellular level. Here, we test the feasibility of a focal stimulation approach using stimulated emission depletion/reversible saturable optical fluorescence transitions-like illumination, whereby switchable light-gated channels are focally activated by a laser beam of one wavelength and deactivated by an overlapping donut-shaped beam of a different wavelength, confining activation to a center focal region. This method requires that activated channelrhodopsins are inactivated by overlapping illumination of a distinct wavelength and that photocurrents are large enough to be detected at the nanoscale. In tests of current optogenetic tools, we found that ChR2 C128A/H134R/T159C and CoChR C108S and C108S/D136A—activated with 405-nm light and inactivated by coillumination with 594-nm light—and C1V1 E122T/C167S—activated by 561-nm light and inactivated by 405-nm light—were most promising in terms of highest photocurrents and efficient inactivation with coillumination. Although further engineering of step-function channelrhodopsin variants with higher photoconductances will be required to employ this approach at the nanoscale, our findings provide a framework to guide future development of this technique.

Speckle contrast imaging allows in vivo imaging of relative blood flow changes. Multiple exposure speckle imaging (MESI) is more accurate than the standard single-exposure method since it allows separating the contribution of the static and moving scatters of the recorded speckle patterns. MESI requires experimental validation on phantoms prior to in vivo experiments to ensure the proper calibration of the system and the robustness of the model. The data analysis relies on the calculation of the speckle contrast for each exposure and a subsequent nonlinear fit to the MESI model to extract the scatterers correlation time and the relative contribution of moving scatters. We have designed two multichannel polydimethylsiloxane chips to study the influence of multiple and static scattering on the accuracy of MESI quantitation. We also propose a method based on standard C++ libraries to implement a computationally efficient analysis of the MESI data. Finally, the system was used to obtain in vivo hemodynamic data on two distinct sensory areas of the mice brain: the barrel cortex and the olfactory bulb.

Light sheet fluorescence microscopy (LSFM) is a powerful tool for investigating model organisms including zebrafish. However, due to scattering and refractive index variations within the sample, the resulting image often suffers from low contrast. Structured illumination (SI) has been combined with scanned LSFM to remove out-of-focus and scattered light using square-law detection. Here, we demonstrate that the combination of LSFM with linear reconstruction SI can further increase resolution and contrast in the vertical and axial directions compared to the widely adopted root-mean square reconstruction method while using the same input images. We apply this approach to imaging neural activity in 7-day postfertilization zebrafish larvae. We imaged two-dimensional sections of the zebrafish central nervous system in two colors at an effective frame rate of 7 frames per second.