Useful Scripts

https://github.com/CarolineMagnain/OpticalCore

 

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Selected Bibliography fro the Martinos Center

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Two-Photon Microscopy

Principle and Review papers:

 

PO₂ imaging

• • Li B, Esipova TV, Sencan I, Kiliç K, Fu B, Desjardins M, Moeini M, Kura S, Yaseen MA, Lesage F, Østergaard L, Devor A, Boas DA, Vinogradov SA, Sakadžic S. More homogeneous capillary flow and oxygenation in deeper cortical layers correlate with increased oxygen extraction. Elife. 2019 07 15; 8.
  • Sencan I, Esipova TV, Yaseen MA, Fu B, Boas DA, Vinogradov SA, Shahidi M, Sakadžic S. Two-photon phosphorescence lifetime microscopy of retinal capillary plexus oxygenation in mice. J Biomed Opt. 2018 12; 23(12):1-9.
  • Kisler K, Nelson AR, Rege SV, Ramanathan A, Wang Y, Ahuja A, Lazic D, Tsai PS, Zhao Z, Zhou Y, Boas DA, Sakadžic S, Zlokovic BV. Pericyte degeneration leads to neurovascular uncoupling and limits oxygen supply to brain. Nat Neurosci. 2017 Mar; 20(3):406-416.
  • Sakadžic S, Mandeville ET, Gagnon L, Musacchia JJ, Yaseen MA, Yucel MA, Lefebvre J, Lesage F, Dale AM, Eikermann-Haerter K, Ayata C, Srinivasan VJ, Lo EH, Devor A, Boas DA. Large arteriolar component of oxygen delivery implies a safe margin of oxygen supply to cerebral tissue. Nat Commun. 2014 Dec 08; 5:5734.
  • Yaseen MA, Srinivasan VJ, Sakadžic S, Radhakrishnan H, Gorczynska I, Wu W, Fujimoto JG, Boas DA. Microvascular oxygen tension and flow measurements in rodent cerebral cortex during baseline conditions and functional activation. J Cereb Blood Flow Metab. 2011 Apr; 31(4):1051-63.
  • Sakadzic S, Roussakis E, Yaseen MA, Mandeville ET, Srinivasan VJ, Arai K, Ruvinskaya S, Devor A, Lo EH, Vinogradov SA, Boas DA. Two-photon high-resolution measurement of partial pressure of oxygen in cerebral vasculature and tissue. Nat Methods. 2010 Sep; 7(9):755-9.

 

NADH imaging

• • Gómez CA, Sutin J, Wu W, Fu B, Uhlirova H, Devor A, Boas DA, Sakadžic S, Yaseen MA. Phasor analysis of NADH FLIM identifies pharmacological disruptions to mitochondrial metabolic processes in the rodent cerebral cortex. PLoS One. 2018; 13(3):e0194578.
  • Yaseen MA, Sakadžic S, Wu W, Becker W, Kasischke KA, Boas DA. In vivo imaging of cerebral energy metabolism with two-photon fluorescence lifetime microscopy of NADH. Biomed Opt Express. 2013 Feb 01; 4(2):307-21.
  • Baraghis E, Devor A, Fang Q, Srinivasan VJ, Wu W, Lesage F, Ayata C, Kasischke KA, Boas DA, Sakadzic S. Two-photon microscopy of cortical NADH fluorescence intensity changes: correcting contamination from the hemodynamic response. J Biomed Opt. 2011 Oct; 16(10):106003.

 

Deep RBC flux imaging

• • Li B, Ohtomo R, Thunemann M, Adams SR, Yang J, Fu B, Yaseen MA, Ran C, Polimeni JR, Boas DA, Devor A, Lo EH, Arai K, Sakadžic S. Two-photon microscopic imaging of capillary red blood cell flux in mouse brain reveals vulnerability of cerebral white matter to hypoperfusion. J Cereb Blood Flow Metab. 2019 Mar 04;

 

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Optical Coherence Tomography

Principle and Review papers:

• • Huang D, Swanson EA,  Lin CP, Schuman JS, Stinson WG, Chang W, Hee MR, Flotte T, Gregory K, Puliafito CA, Fujimoto JG. Optical coherence tomography Science 254.5035 (1991): 1178-1181.
  • Fercher AF, Drexler W, Hitzenberger CK, Lasser T. Optical coherence tomography-principles and applications. Reports on progress in physics, 66(2), 239, 2003.

 

In vivo imaging

• • Srinivasan VJ, Sakadzic S, Gorczynska I, Ruvinskaya S, Wu W, Fujimoto JG, Boas DA. Depth-resolved microscopy of cortical hemodynamics with optical coherence tomography. Opt Lett. 2009 Oct 15; 34(20):3086-8.
  • Srinivasan VJ, Sakadzic S, Gorczynska I, Ruvinskaya S, Wu W, Fujimoto JG, Boas DA. Quantitative cerebral blood flow with optical coherence tomography. Opt Express. 2010 Feb 01; 18(3):2477-94.
  • Srinivasan VJ, Mandeville ET, Can A, Blasi F, Climov M, Daneshmand A, Lee JH, Yu E, Radhakrishnan H, Lo EH, Sakadžic S, Eikermann-Haerter K, Ayata C. Multiparametric, longitudinal optical coherence tomography imaging reveals acute injury and chronic recovery in experimental ischemic stroke. PLoS One. 2013; 8(8):e71478.
  • Li B, Wang H, Fu B, Wang R, Sakadžic S, Boas DA. Impact of temporal resolution on estimating capillary RBC-flux with optical coherence tomography. J Biomed Opt. 2017 01 01; 22(1):16014.

 

Ex vivo imaging 

• • Magnain C, Augustinack JC, Reuter M, Wachinger C, Frosch MP, Ragan T, Akkin T, Wedeen VJ, Boas DA, and Fischl B. Blockface histology with optical coherence tomography: a comparison with Nissl staining. NeuroImage 84 (2014): 524-533.
  • Magnain C, Augustinack JC, Konukoglu E, Frosch MP, Sakadžić S, Varjabedian A, Garcia N, Wedeen VJ, Boas DA, Fischl B. Optical coherence tomography visualizes neurons in human entorhinal cortex. Neurophotonics2.1 (2015): 015004.
  • Wang H, Magnain C, Sakadžić S, Fischl B, Boas DA. Characterizing the optical properties of human brain tissue with high numerical aperture optical coherence tomography. Biomedical optics express 8.12 (2017): 5617-5636.
  • Magnain C, Augustinack JC, Tirrell L, Fogarty M, Frosch MP, Boas DA, Fischl B, Rockland KS. Colocalization of neurons in optical coherence microscopy and Nissl-stained histology in Brodmann’s area 32 and area 21. Brain Structure and Function 224.1 (2019): 351-362.

 

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Speckle / Multispectral Imaging

• • Shvedova M, Litvak MM, Roberts JD, Fukumura D, Suzuki T, Sencan I, Li G, Reventun P, Buys ES, Kim HH, Sakadžic S, Ayata C, Huang PL, Feil R, Atochin DN. cGMP-dependent protein kinase I in vascular smooth muscle cells improves ischemic stroke outcome in mice. J Cereb Blood Flow Metab. 2019 Aug 18
  • Xie H, Chung DY, Kura S, Sugimoto K, Aykan SA, Wu Y, Sakadžic S, Yaseen MA, Boas DA, Ayata C. Differential effects of anesthetics on resting state functional connectivity in the mouse. J Cereb Blood Flow Metab. 2019 May 15;
  • Kura S, Xie H, Fu B, Ayata C, Boas DA, Sakadžic S. Intrinsic optical signal imaging of the blood volume changes is sufficient for mapping the resting state functional connectivity in the rodent cortex. J Neural Eng. 2018 06; 15(3):035003.
  • von Bornstädt D, Houben T, Seidel JL, Zheng Y, Dilekoz E, Qin T, Sandow N, Kura S, Eikermann-Haerter K, Endres M, Boas DA, Moskowitz MA, Lo EH, Dreier JP, Woitzik J, Sakadžic S, Ayata C. Supply-demand mismatch transients in susceptible peri-infarct hot zones explain the origins of spreading injury depolarizations. Neuron. 2015 Mar 04; 85(5):1117-31.
  • Yuzawa I, Sakadžic S, Srinivasan VJ, Shin HK, Eikermann-Haerter K, Boas DA, Ayata C. Cortical spreading depression impairs oxygen delivery and metabolism in mice. J Cereb Blood Flow Metab. 2012 Feb; 32(2):376-86.