Structured illumination diffuse optical tomography for noninvasive functional neuroimaging in mice

Unrolled-DOT: an interpretable deep network for diffuse optical tomography

Significance

Imaging through scattering media is critical in many biomedical imaging applications, such as breast tumor detection and functional neuroimaging. Time-of-flight diffuse optical tomography (ToF-DOT) is one of the most promising methods for high-resolution imaging through scattering media. ToF-DOT and many traditional DOT methods require an image reconstruction algorithm. Unfortunately, this algorithm often requires long computational runtimes and may produce lower quality reconstructions in the presence of model mismatch or improper hyperparameter tuning.

Aim

We used a data-driven unrolled network as our ToF-DOT inverse solver. The unrolled network is faster than traditional inverse solvers and achieves higher reconstruction quality by accounting for model mismatch.

Approach

Our model "Unrolled-DOT" uses the learned iterative shrinkage thresholding algorithm. In addition, we incorporate a refinement U-Net and Visual Geometry Group (VGG) perceptual loss to further increase the reconstruction quality. We trained and tested our model on simulated and real-world data and benchmarked against physics-based and learning-based inverse solvers.

Results

In experiments on real-world data, Unrolled-DOT outperformed learning-based algorithms and achieved over 10× reduction in runtime and mean-squared error, compared to traditional physics-based solvers.

Conclusion

We demonstrated a learning-based ToF-DOT inverse solver that achieves state-of-the-art performance in speed and reconstruction quality, which can aid in future applications for noninvasive biomedical imaging.

Homotopic contralesional excitation suppresses spontaneous circuit repair and global network reconnections following ischemic stroke

Understanding circuit-level manipulations that affect the brain's capacity for plasticity will inform the design of targeted interventions that enhance recovery after stroke. Following stroke, increased contralesional activity (e.g. use of the unaffected limb) can negatively influence recovery, but it is unknown which specific neural connections exert this influence, and to what extent increased contralesional activity affects systems- and molecular-level biomarkers of recovery. Here, we combine optogenetic photostimulation with optical intrinsic signal imaging to examine how contralesional excitatory activity affects cortical remodeling after stroke in mice. Following photothrombosis of left primary somatosensory forepaw (S1FP) cortex, mice either recovered spontaneously or received chronic optogenetic excitation of right S1FP over the course of 4 weeks. Contralesional excitation suppressed perilesional S1FP remapping and was associated with abnormal patterns of stimulus-evoked activity in the unaffected limb. This maneuver also prevented the restoration of resting-state functional connectivity (RSFC) within the S1FP network, RSFC in several networks functionally distinct from somatomotor regions, and resulted in persistent limb-use asymmetry. In stimulated mice, perilesional tissue exhibited transcriptional changes in several genes relevant for recovery. Our results suggest that contralesional excitation impedes local and global circuit reconnection through suppression of cortical activity and several neuroplasticity-related genes after stroke, and highlight the importance of site selection for targeted therapeutic interventions after focal ischemia.

Simple demodulation method for optical property extraction in spatial frequency domain imaging

Different demodulation methods affect the efficiency and accuracy of spatial frequency domain imaging (SFDI). A simple and effective method of sum-to-product identities (STPI) demodulation was proposed in this study. STPI requires one fewer image than conventional three-phase demodulation (TPD) at a spatial frequency. Numerical simulation and phantom experiments were performed. The result proved the feasibility of STPI and showed that STPI combined with subtraction can achieve high-precision demodulation in the low spatial frequency domain. Through extraction of phantom optical properties, STPI had similar accuracy compared with other demodulation methods in extracting optical properties in phantoms. STPI was also used to extract the optical properties of milk, and it had highly consistent results with TPD, which can distinguish milk with different fat content. The demodulation effect of this method in the low spatial frequencies is better than other fast demodulation methods.

In vivo voltage-sensitive dye imaging of mouse cortical activity with mesoscopic optical tomography

Significance: Cellular layering is a hallmark of the mammalian neocortex with layer and cell type-specific connections within the cortical mantle and subcortical connections. A key challenge in studying circuit function within the neocortex is to understand the spatial and temporal patterns of information flow between different columns and layers. Aim: We aimed to investigate the three-dimensional (3D) layer- and area-specific interactions in mouse cortex in vivo. Approach: We applied a new promising neuroimaging method-fluorescence laminar optical tomography in combination with voltage-sensitive dye imaging (VSDi). VSDi is a powerful technique for interrogating membrane potential dynamics in assemblies of cortical neurons, but it is traditionally used for two-dimensional (2D) imaging. Our mesoscopic technique allows visualization of neuronal activity in a 3D manner with high temporal resolution. Results: We first demonstrated the depth-resolved capability of 3D mesoscopic imaging technology in Thy1-ChR2-YFP transgenic mice. Next, we recorded the long-range functional projections between sensory cortex (S1) and motor cortex (M1) in mice, in vivo, following single whisker deflection. Conclusions: The results show that mesoscopic imaging technique has the potential to investigate the layer-specific neural connectivity in the mouse cortex in vivo. Combination of mesoscopic imaging technique with optogenetic control strategy is a promising platform for determining depth-resolved interactions between cortical circuit elements.

Spatial frequency domain imaging for the longitudinal monitoring of vascularization during mouse femoral graft healing

Allograft is the current gold standard for treating critical-sized bone defects. However, allograft healing is usually compromised partially due to poor host-mediated vascularization. In the efforts towards developing new methods to enhance allograft healing, a non-terminal technique for monitoring the vascularization is needed in pre-clinical mouse models. In this study, we developed a non-invasive instrument based on spatial frequency domain imaging (SFDI) for longitudinal monitoring of the mouse femoral graft healing. SFDI technique provided total hemoglobin concentration (THC) and oxygen saturation (StO2) of the graft and the surrounding soft tissues. SFDI measurements were performed from 1 day before to 44 days after graft transplantation. Autograft, another type of bone graft with higher vascularization potential was also measured as a comparison to allograft. For both grafts, the overall temporal changes of the measured THC agreed with the physiological expectations of vascularization timeline during bone healing. A significantly greater increase in THC was observed in the autograft group compared to the allograft group, which agreed with the expectation that allografts have more compromised vascularization.

Monitoring of Stimulus Evoked Murine Somatosensory Cortex Hemodynamic Activity With Volumetric Multi-Spectral Optoacoustic Tomography

Sensory stimulation is an attractive paradigm for studying brain activity using various optical-, ultrasound- and MRI-based functional neuroimaging methods. Optoacoustics has been recently suggested as a powerful new tool for scalable mapping of multiple hemodynamic parameters with rich contrast and previously unachievable spatio-temporal resolution. Yet, its utility for studying the processing of peripheral inputs at the whole brain level has so far not been quantified. We employed volumetric multi-spectral optoacoustic tomography (vMSOT) to non-invasively monitor the HbO, HbR, and HbT dynamics across the mouse somatosensory cortex evoked by electrical paw stimuli. We show that elevated contralateral activation is preserved in the HbO map (invisible to MRI) under isoflurane anesthesia. Brain activation is shown to be predominantly confined to the somatosensory cortex, with strongest activation in the hindpaw region of the contralateral sensorimotor cortex. Furthermore, vMSOT detected the presence of an initial dip in the contralateral hindpaw region in the delta HbO channel. Sensorimotor cortical activity was identified over all other regions in HbT and HbO but not in HbR. Pearson’s correlation mapping enabled localizing the response to the sensorimotor cortex further highlighting the ability of vMSOT to bridge over imaging performance deficiencies of other functional neuroimaging modalities.

Altered hemodynamics contribute to local but not remote functional connectivity disruption due to glioma growth

Glioma growth can cause pervasive changes in the functional connectivity (FC) of brain networks, which has been associated with re-organization of brain functions and development of functional deficits in patients. Mechanisms underlying functional re-organization in brain networks are not understood and efforts to utilize functional imaging for surgical planning, or as a biomarker of functional outcomes are confounded by the heterogeneity in available human data. Here we apply multiple imaging modalities in a well-controlled murine model of glioma with extensive validation using human data to explore mechanisms of FC disruption due to glioma growth. We find gliomas cause both local and distal changes in FC. FC changes in networks proximal to the tumor occur secondary to hemodynamic alterations but surprisingly, remote FC changes are independent of hemodynamic mechanisms. Our data strongly implicate hemodynamic alterations as the main driver of local changes in measurements of FC in patients with glioma.

Spatial frequency domain imaging in 2019: principles, applications, and perspectives

Spatial frequency domain imaging (SFDI) has witnessed very rapid growth over the last decade, owing to its unique capabilities for imaging optical properties and chromophores over a large field-of-view and in a rapid manner. We provide a comprehensive review of the principles of this imaging method as of 2019, review the modeling of light propagation in this domain, describe acquisition methods, provide an understanding of the various implementations and their practical limitations, and finally review applications that have been published in the literature. Importantly, we also introduce a group effort by several key actors in the field for the dissemination of SFDI, including publications, advice in hardware and implementations, and processing code, all freely available online.

Spatial frequency domain imaging in 2019: principles, applications, and perspectives

Spatial frequency domain imaging (SFDI) has witnessed very rapid growth over the last decade, owing to its unique capabilities for imaging optical properties and chromophores over a large field-of-view and in a rapid manner. We provide a comprehensive review of the principles of this imaging method as of 2019, review the modeling of light propagation in this domain, describe acquisition methods, provide an understanding of the various implementations and their practical limitations, and finally review applications that have been published in the literature. Importantly, we also introduce a group effort by several key actors in the field for the dissemination of SFDI, including publications, advice in hardware and implementations, and processing code, all freely available online.

Review of structured light in diffuse optical imaging

Diffuse optical imaging probes deep living tissue enabling structural, functional, metabolic, and molecular imaging. Recently, due to the availability of spatial light modulators, wide-field quantitative diffuse optical techniques have been implemented, which benefit greatly from structured light methodologies. Such implementations facilitate the quantification and characterization of depth-resolved optical and physiological properties of thick and deep tissue at fast acquisition speeds. We summarize the current state of work and applications in the three main techniques leveraging structured light: spatial frequency-domain imaging, optical tomography, and single-pixel imaging. The theory, measurement, and analysis of spatial frequency-domain imaging are described. Then, advanced theories, processing, and imaging systems are summarized. Preclinical and clinical applications on physiological measurements for guidance and diagnosis are summarized. General theory and method development of tomographic approaches as well as applications including fluorescence molecular tomography are introduced. Lastly, recent developments of single-pixel imaging methodologies and applications are reviewed.

Effective Connectivity Measured Using Optogenetically Evoked Hemodynamic Signals Exhibits Topography Distinct from Resting State Functional Connectivity in the Mouse

Brain connectomics has expanded from histological assessment of axonal projection connectivity (APC) to encompass resting state functional connectivity (RS-FC). RS-FC analyses are efficient for whole-brain mapping, but attempts to explain aspects of RS-FC (e.g., interhemispheric RS-FC) based on APC have been only partially successful. Neuroimaging with hemoglobin alone lacks specificity for determining how activity in a population of cells contributes to RS-FC. Wide-field mapping of optogenetically defined connectivity could provide insights into the brain's structure-function relationship. We combined optogenetics with optical intrinsic signal imaging to create an efficient, optogenetic effective connectivity (Opto-EC) mapping assay. We examined EC patterns of excitatory neurons in awake, Thy1-ChR2 transgenic mice. These Thy1-based EC (Thy1-EC) patterns were evaluated against RS-FC over the cortex. Compared to RS-FC, Thy1-EC exhibited increased spatial specificity, reduced interhemispheric connectivity in regions with strong RS-FC, and appreciable connection strength asymmetry. Comparing the topography of Thy1-EC and RS-FC patterns to maps of APC revealed that Thy1-EC more closely resembled APC than did RS-FC. The more general method of Opto-EC mapping with hemoglobin can be determined for 100 sites in single animals in under an hour, and is amenable to other neuroimaging modalities. Opto-EC mapping represents a powerful strategy for examining evolving connectivity-related circuit plasticity.

Lightweight sCMOS-based high-density diffuse optical tomography

Though optical imaging of human brain function is gaining momentum, widespread adoption is restricted in part by a tradeoff among cap wearability, field of view, and resolution. To increase coverage while maintaining functional magnetic resonance imaging (fMRI)-comparable image quality, optical systems require more fibers. However, these modifications drastically reduce the wearability of the imaging cap. The primary obstacle to optimizing wearability is cap weight, which is largely determined by fiber diameter. Smaller fibers collect less light and lead to challenges in obtaining adequate signal-to-noise ratio. Here, we report on a design that leverages the exquisite sensitivity of scientific CMOS cameras to use fibers with ∼30× smaller cross-sectional area than current high-density diffuse optical tomography (HD-DOT) systems. This superpixel sCMOS DOT (SP-DOT) system uses 200-μm -diameter fibers that facilitate a lightweight, wearable cap. We developed a superpixel algorithm with pixel binning and electronic noise subtraction to provide high dynamic range ( >105 ), high frame rate ( >6  Hz ), and a low effective detectivity threshold ( ∼200  fW/Hz1/2-mm2 ), each comparable with previous HD-DOT systems. To assess system performance, we present retinotopic mapping of the visual cortex ( n=5 subjects). SP-DOT offers a practical solution to providing a wearable, large field-of-view, and high-resolution optical neuroimaging system.