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White BR, Adepoju TE, Fisher HB, Shinohara RT, Vandekar S. Spatial nonstationarity of image noise in widefield optical imaging and its effects on cluster-based inference for resting-state functional connectivity. J Neurosci Methods 2024; 404:110076. [PMID: 38331258 PMCID: PMC10940215 DOI: 10.1016/j.jneumeth.2024.110076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 02/04/2024] [Indexed: 02/10/2024]
Abstract
BACKGROUND Resting-state functional connectivity (RSFC) analysis with widefield optical imaging (WOI) is a potentially powerful tool to develop imaging biomarkers in mouse models of disease before translating them to human neuroimaging with functional magnetic resonance imaging (fMRI). The delineation of such biomarkers depends on rigorous statistical analysis. However, statistical understanding of WOI data is limited. In particular, cluster-based analysis of neuroimaging data depends on assumptions of spatial stationarity (i.e., that the distribution of cluster sizes under the null is equal at all brain locations). Whether actual data deviate from this assumption has not previously been examined in WOI. NEW METHOD In this manuscript, we characterize the effects of spatial nonstationarity in WOI RSFC data and adapt a "two-pass" technique from fMRI to correct cluster sizes and mitigate spatial bias, both parametrically and nonparametrically. These methods are tested on multi-institutional data. RESULTS AND COMPARISON WITH EXISTING METHODS We find that spatial nonstationarity has a substantial effect on inference in WOI RSFC data with false positives much more likely at some brain regions than others. This pattern of bias varies between imaging systems, contrasts, and mouse ages, all of which could affect experimental reproducibility if not accounted for. CONCLUSIONS Both parametric and nonparametric corrections for nonstationarity result in significant improvements in spatial bias. The proposed methods are simple to implement and will improve the robustness of inference in optical neuroimaging data.
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Affiliation(s)
- Brian R White
- Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Division of Cardiology, Department of Pediatrics, USA.
| | - Temilola E Adepoju
- Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Division of Cardiology, Department of Pediatrics, USA
| | - Hayden B Fisher
- Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Division of Cardiology, Department of Pediatrics, USA
| | - Russell T Shinohara
- University of Pennsylvania, Perelman School of Medicine, Department of Biostatistics, Epidemiology, and Informatics, USA; University of Pennsylvania, Center for Biomedical Image Computing and Analysis, Department of Radiology, USA; University of Pennsylvania, Penn Statistics in Imaging and Visualization Endeavor, Department of Biostatistics, Epidemiology, and Informatics, USA
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Liu B, Shah S, Küreli G, Devor A, Boas DA, Cheng X. Measurements of slow tissue dynamics with short-separation speckle contrast optical spectroscopy. BIOMEDICAL OPTICS EXPRESS 2023; 14:4790-4799. [PMID: 37791271 PMCID: PMC10545176 DOI: 10.1364/boe.497604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 10/05/2023]
Abstract
Laser speckle contrast imaging (LSCI) measures 2D maps of cerebral blood flow (CBF) in small animal brains such as mice. The contrast measured in LSCI also includes the static and slow-varying components that contain information about brain tissue dynamics. But these components are less studied as compared to the fast dynamics of CBF. In traditional wide-field LSCI, the contrast measured in the tissue is largely contaminated by neighboring blood vessels, which reduces the sensitivity to these static and slow components. Our goal is to enhance the sensitivity of the contrast to static and slow tissue dynamics and test models to quantify the characteristics of these components. To achieve this, we have developed a short-separation speckle contrast optical spectroscopy (ss-SCOS) system by implementing point illumination and point detection using multi-mode fiber arrays to enhance the static and slow components in speckle contrast measurements as compared to traditional wide-field LSCI (WF-LSCI). We observed larger fractions of the static and slow components when measured in the tissue using ss-SCOS than in traditional LSCI for the same animal and region of interest. We have also established models to obtain the fractions of the static and slow components and quantify the decorrelation time constants of the intensity auto-correlation function for both fast blood flow and slower tissue dynamics. Using ss-SCOS, we demonstrate the variations of fast and slow brain dynamics in animals before and post-stroke, as well as within an hour post-euthanasia. This technique establishes the foundation to measure brain tissue dynamics other than CBF, such as intracellular motility.
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Affiliation(s)
- Bingxue Liu
- Neurophotonics Center, Boston University, Boston, Massachusetts 02215, USA
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, USA
| | - Shashwat Shah
- Neurophotonics Center, Boston University, Boston, Massachusetts 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
| | - Gülce Küreli
- Neurophotonics Center, Boston University, Boston, Massachusetts 02215, USA
| | - Anna Devor
- Neurophotonics Center, Boston University, Boston, Massachusetts 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
| | - David A. Boas
- Neurophotonics Center, Boston University, Boston, Massachusetts 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
| | - Xiaojun Cheng
- Neurophotonics Center, Boston University, Boston, Massachusetts 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
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Giblin J, Kura S, Nunuez JLU, Zhang J, Kureli G, Jiang J, Boas DA, Chen IA. High throughput detection of capillary stalling events with Bessel beam two-photon microscopy. NEUROPHOTONICS 2023; 10:035009. [PMID: 37705938 PMCID: PMC10495839 DOI: 10.1117/1.nph.10.3.035009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 08/09/2023] [Accepted: 08/17/2023] [Indexed: 09/15/2023]
Abstract
Significance Brief disruptions in capillary flow, commonly referred to as capillary "stalling," have gained interest recently for their potential role in disrupting cerebral blood flow and oxygen delivery. Approaches to studying this phenomenon have been hindered by limited volumetric imaging rates and cumbersome manual analysis. The ability to precisely and efficiently quantify the dynamics of these events will be key in understanding their potential role in stroke and neurodegenerative diseases, such as Alzheimer's disease. Aim Our study aimed to demonstrate that the fast volumetric imaging rates offered by Bessel beam two-photon microscopy combined with improved data analysis throughput allows for faster and more precise measurement of capillary stall dynamics. Results We found that while our analysis approach was unable to achieve full automation, we were able to cut analysis time in half while also finding stalling events that were missed in traditional blind manual analysis. The resulting data showed that our Bessel beam system was captured more stalling events compared to optical coherence tomography, particularly shorter stalling events. We then compare differences in stall dynamics between a young and old group of mice as well as a demonstrate changes in stalling before and after photothrombotic model of stroke. Finally, we also demonstrate the ability to monitor arteriole dynamics alongside stall dynamics. Conclusions Bessel beam two-photon microscopy combined with high throughput analysis is a powerful tool for studying capillary stalling due to its ability to monitor hundreds of capillaries simultaneously at high frame rates.
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Affiliation(s)
- John Giblin
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
- Boston University, Neurophotonics Center, Boston, Massachusetts, United States
| | - Sreekanth Kura
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
- Boston University, Neurophotonics Center, Boston, Massachusetts, United States
| | - Juan Luis Ugarte Nunuez
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
- Boston University, Neurophotonics Center, Boston, Massachusetts, United States
| | - Juncheng Zhang
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
- Boston University, Neurophotonics Center, Boston, Massachusetts, United States
| | - Gulce Kureli
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
- Boston University, Neurophotonics Center, Boston, Massachusetts, United States
| | - John Jiang
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
- Boston University, Neurophotonics Center, Boston, Massachusetts, United States
| | - David A. Boas
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
- Boston University, Neurophotonics Center, Boston, Massachusetts, United States
| | - Ichun A. Chen
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
- Boston University, Neurophotonics Center, Boston, Massachusetts, United States
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Sunil S, Jiang J, Shah S, Kura S, Kilic K, Erdener SE, Ayata C, Devor A, Boas DA. Neurovascular coupling is preserved in chronic stroke recovery after targeted photothrombosis. Neuroimage Clin 2023; 38:103377. [PMID: 36948140 PMCID: PMC10034641 DOI: 10.1016/j.nicl.2023.103377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/17/2023]
Abstract
Functional neuroimaging, which measures hemodynamic responses to brain activity, has great potential for monitoring recovery in stroke patients and guiding rehabilitation during recovery. However, hemodynamic responses after stroke are almost always altered relative to responses in healthy subjects and it is still unclear if these alterations reflect the underlying brain physiology or if the alterations are purely due to vascular injury. In other words, we do not know the effect of stroke on neurovascular coupling and are therefore limited in our ability to use functional neuroimaging to accurately interpret stroke pathophysiology. To address this challenge, we simultaneously captured neural activity, through fluorescence calcium imaging, and hemodynamics, through intrinsic optical signal imaging, during longitudinal stroke recovery. Our data suggest that neurovascular coupling was preserved in the chronic phase of recovery (2 weeks and 4 weeks post-stoke) and resembled pre-stroke neurovascular coupling. This indicates that functional neuroimaging faithfully represents the underlying neural activity in chronic stroke. Further, neurovascular coupling in the sub-acute phase of stroke recovery was predictive of long-term behavioral outcomes. Stroke also resulted in increases in global brain oscillations, which showed distinct patterns between neural activity and hemodynamics. Increased neural excitability in the contralesional hemisphere was associated with increased contralesional intrahemispheric connectivity. Additionally, sub-acute increases in hemodynamic oscillations were associated with improved sensorimotor outcomes. Collectively, these results support the use of hemodynamic measures of brain activity post-stroke for predicting functional and behavioral outcomes.
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Affiliation(s)
- Smrithi Sunil
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.
| | - John Jiang
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Shashwat Shah
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Sreekanth Kura
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Kivilcim Kilic
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Sefik Evren Erdener
- Institute of Neurological Sciences and Psychiatry, Hacettepe University, Ankara, Turkey
| | - Cenk Ayata
- Departments of Neurology and Radiology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Anna Devor
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA 02114, USA
| | - David A Boas
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.
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