Software

We are developing tools for biomedical imaging including microscopy as well as human brain measurements. If you have a particular research question regarding wave propagation or light scattering in biological tissue, you are welcome to discuss it with us! Contact: xcheng17@bu.edu

Dynamic speckle model:

A fast way to compute speckle pattern evolution. It is useful for speckle-based techniques such as laser speckle contrast imaging (LSCI) and speckle contrast optical spectroscopy (SCOS).

https://github.com/BUNPC/DynamicSpeckleModel

Cite paper: Zilpelwar S, Sie EJ, Postnov D, Chen AI, Zimmermann B, Marsili F, Boas DA, Cheng X. Model of dynamic speckle evolution for evaluating laser speckle contrast measurements of tissue dynamics. Biomedical Optics Express. 2022 Dec 1;13(12):6533-49.

Beam propagation model:

Our model based on the beam propagation method calculates the wave propagation in the scattering medium. 

https://github.com/BUNPC/Beam-Propagation-Method

Cite paper: Cheng X, Li Y, Mertz J, Sakadžić S, Devor A, Boas DA, Tian L. Development of a beam propagation method to simulate the point spread function degradation in scattering media. Optics letters. 2019 Oct 15;44(20):4989-92.

Monte Carlo wave model:

It combines Monte Carlo simulation (photon picture) with wave propagation that calculates the traditional and time-domain DCS signals from first principles.

https://github.com/BUNPC/MonteCarloWaveModel

Cite paper: Cheng X, Chen H, Sie EJ, Marsili F, Boas DA. Development of a Monte Carlo-wave model to simulate time-domain diffuse correlation spectroscopy measurements from first principles. Journal of Biomedical Optics. 2022 Aug 1;27(8):083009-.

Vascular Anatomical Network Model:

The vascular anatomical network (VAN) model computes oxygen distribution, blood flow distribution and BOLD fMRI signals within mouse microvascular stacks obtained from in-vivo two-photon microscopy.

https://github.com/BUNPC/VAN_modeling

Cite papers:

Cheng, X., Berman, A.J.L.J., Polimeni, J.R., Buxton, R.B., Gagnon, L., Devor, A., Sakadžić, S., and Boas, D.A., “Dependence of the MR signal on the magnetic susceptibility of blood studied with models based on real microvascular networks.,” Magnetic resonance in medicine (2019).

Gagnon, L., Sakadžić, S., Lesage, F., Pouliot, P., Dale, A.M., Devor, A., Buxton, R.B., and Boas, D.A., “Validation and optimization of hypercapnic-calibrated fMRI from oxygen-sensitive two-photon microscopy.,” Philosophical transactions of the Royal Society of London. Series B, Biological sciences 371(1705), 20150359 (2016).

Gagnon, L., Sakadžić, S., Lesage, F., Musacchia, J.J., Lefebvre, J., Fang, Q., Yücel, M.A., Evans, K.C., Mandeville, E.T., et al., “Quantifying the microvascular origin of BOLD-fMRI from first principles with two-photon microscopy and an oxygen-sensitive nanoprobe.,” The Journal of neuroscience : the official journal of the Society for Neuroscience 35(8), 3663–3675 (2015).