19) Wei, Xiang, Tristan T. Hormel, Shaohua Pi, Bingjie Wang, John C. Morrison, and Yali Jia. "Wide-field sensorless adaptive optics swept-source optical coherence tomographic angiography in rodents." Optics Letters 47, no. 19 (2022): 5060-5063.

18) Shaohua Pi, Tristan T. Hormel, Bingjie Wang, Steven T. Bailey, Thomas S. Hwang, David Huang, John C. Morrison, and Yali Jia, "Volume-based, layer-independent, disease-agnostic detection of abnormal retinal reflectivity, nonperfusion, and neovascularization using structural and angiographic OCT," Biomed. Opt. Express 13, 4889-4906 (2022).

First steps to identify 3-D map of retinal ischemia and establish universal pathology index

Fig. 1 Demonstration of OCT scan registration in different subjects. (A) Lateral registration was achieved by foveal center alignment in a 9×9-mm image, with the nasal side flipped in the left eyes to match with the right eyes. (B) Axial registration is achieved by axially normalizing the A-lines according to percent retinal depth.

Fig. 2 Demonstration of 3-D detection of nonperfusion. The perfusion volume simulated by convoluting the angiogram volume with 3-D Gaussian kernel, and then compared between reference and diseased retinas using Eq. (2) to calculate the 3-D nonperfusion map. The 3-D nonperfusion map is color-coded by percent retinal depth (ILM: 0, BM: 100).

Fig. 3 Diagnostic power of various pathology indexes to differentiate non-referable DR from referable DR subjects. The pathology index for each clinical feature was calculated as the decibel ratio of the averaged deviation magnitude from a target retinal scan (Pd) to baselines (Ph) from healthy subjects. (A) The combined pathology index achieved an R=0.95 Spearman correlation coefficient with the DR severity. The black dotted line indicates a pathology index cut-off PI=6 corresponding to the best diagnostic point in B. (B) Receiver operating characteristic curves for the pathology indexes of each clinical feature, and the combined one for referable vs. non-referable DR classification. The optimal operating point of the ROC curve for the averaged PI was determined as 1-specificity= 0.28 and sensitivity=0.87, output from the parameter OPTROCPT of the MATLAB function perfcurve( ).


17) Guo, Yukun, Tristan T. Hormel, Shaohua Pi, Xiang Wei, Min Gao, John C. Morrison, and Yali Jia. "An end-to-end network for segmenting the vasculature of three retinal capillary plexuses from OCT angiographic volumes." Biomedical Optics Express 12, no. 8 (2021): 4889-4900.

16) You, Qi Sheng, Ou Tan, Shaohua Pi, Liang Liu, Ping Wei, Aiyin Chen, Eliesa Ing, Yali Jia, and David Huang. "Effect of algorithms and covariates in glaucoma diagnosis with optical coherence tomography angiography." British Journal of Ophthalmology (2021).


15) You, Qi Sheng, Jie Wang, Yukun Guo, Shaohua Pi, Christina J. Flaxel, Steven T. Bailey, David Huang, Yali Jia, and Thomas S. Hwang. "Optical coherence tomography angiography avascular area association with 1-year treatment requirement and disease progression in diabetic retinopathy." American journal of ophthalmology 217 (2020): 268-277.

14) Pi, Shaohua, Tristan T. Hormel, Xiang Wei, William Cepurna, Bingjie Wang, John C. Morrison, and Yali Jia. "Retinal capillary oximetry with visible light optical coherence tomography." Proceedings of the National Academy of Sciences 117, no. 21 (2020): 11658-11666.

First retinal capillary oximetry

Fig. 1 Representative capillary sO2 along with that in major vessels (A: artery, V: vein) in one rat retina responding to regulation in oxygen concentration in inhaled gas, from 21% (normoxia) to 15% (hypoxia), then to 100% (hyperoxia) and to 21% (return to normoxia). The angiogram (2×2-mm) was obtained by averaging all 8 scans at all conditions acquired in the same region. The sO2 in capillary segments corresponded to trends shown by the sO2 in major vessels, which decreased with the reduction of oxygen concentration in the inhaled gas.

Fig. 2 Ultra-wide-field angiogram of rat retinal vessels stitched from multiple scans with smaller field of view.

13) Pi, Shaohua, Tristan T. Hormel, Xiang Wei, William Cepurna, John C. Morrison, and Yali Jia. "Imaging retinal structures at cellular-level resolution by visible-light optical coherence tomography." Optics letters 45, no. 7 (2020): 2107-2110.

In vivo cellular-resolution retinal imaging


12) Pi, Shaohua, Tristan T. Hormel, Xiang Wei, William Cepurna, Acner Camino, Yukun Guo, David Huang, John C. Morrison, and Yali Jia. "Monitoring retinal responses to acute intraocular pressure elevation in rats with visible light optical coherence tomography." Neurophotonics 6, no. 4 (2019): 041104.

The PI's first paper on animal model

Fig. 1 En face images (2.2 × 2.2 mm2) showing retinal vascular perfusion responses to acute IOP elevation

Comprehensive retinal responses to acute IOP elevation

which include retinal oxygen extraction and oxygen metabolism, as well as structural reflectivity, angiography and blood flow, all provided with vis-OCT simultaneously.

11) Wang, Bingjie, Acner Camino, Shaohua Pi, Yukun Guo, Jie Wang, David Huang, Thomas S. Hwang, and Yali Jia. "Three-dimensional structural and angiographic evaluation of foveal ischemia in diabetic retinopathy: method and validation." Biomedical optics express 10, no. 7 (2019): 3522-3532.

10) Wei, Xiang, Tristan T. Hormel, Shaohua Pi, Yukun Guo, Yifan Jian, and Yali Jia. "High dynamic range optical coherence tomography angiography (HDR-OCTA)." Biomedical optics express 10, no. 7 (2019): 3560-3571.

9) Wei, Xiang, Acner Camino, Shaohua Pi, Tristan T. Hormel, William Cepurna, David Huang, John C. Morrison, and Yali Jia. "Real-time cross-sectional and en face OCT angiography guiding high-quality scan acquisition." Optics letters 44, no. 6 (2019): 1431-1434.

8) Pi, Shaohua, Acner Camino, Xiang Wei, Tristan T. Hormel, William Cepurna, John C. Morrison, and Yali Jia. "Automated phase unwrapping in Doppler optical coherence tomography." Journal of biomedical optics 24, no. 1 (2019): 010502.

Invention of automated phase unwrapping algorithm

Fig. 2 Demonstration of phase unwrapping of a vein and an artery affected by phase wrapping, as well as a vein free of phase wrapping.


7) Pi, Shaohua, Acner Camino, Xiang Wei, Joseph Simonett, William Cepurna, David Huang, John C. Morrison, and Yali Jia. "Rodent retinal circulation organization and oxygen metabolism revealed by visible-light optical coherence tomography." Biomedical optics express 9, no. 11 (2018): 5851-5862.

The PI's first demonstration of retinal flow transition pattern in rats

Fig. 1 The 3D schematic vascular network illustrates the flow transition from artery to vein in rat retina with microvasculature architecture corresponding to the current findings.

Fig. 2 Retinal oxygen metabolic rate measurement with visible light OCT.

rTRO2: Retinal oxygen transport rate.

rMRO2: Retinal oxygen metabolic rate.

6) Wei, Xiang, Acner Camino, Shaohua Pi, William Cepurna, David Huang, John C. Morrison, and Yali Jia. "Fast and robust standard-deviation-based method for bulk motion compensation in phase-based functional OCT." Optics letters 43, no. 9 (2018): 2204-2207.

5) Pi, Shaohua, Acner Camino, William Cepurna, Xiang Wei, Miao Zhang, David Huang, John Morrison, and Yali Jia. "Automated spectroscopic retinal oximetry with visible-light optical coherence tomography." Biomedical optics express 9, no. 5 (2018): 2056-2067.

The PI's first OCT oximetry paper

Fig. 1 Logarithmic absorption extinction coefficients of oxygenated hemoglobin (HbO2) and deoxygenated hemoglobin (Hb) in the wavelength range from 400 nm to 1000 nm. The much higher extinction coefficients in the visible range (vis-OCT) compared to the infrared range (standard OCT) provides a better contrast to quantify oxygen saturation (sO2).

Oxygen Saturation

sO2 = CHbO2 / (CHbO2 + CHb)

Oxygen saturation is the fraction of oxygen-saturated hemoglobin relative to total hemoglobin in the blood. If quantified accurately, sO2 could be used as a biomarker to monitor retinal metabolism and provide a valuable early indicator of ocular disease.

Fig. 2 (a)-(c): Arteries demonstrate higher oxygen saturation (sO2) than veins by visible light OCT oximetry. Red: artery. Green: vein. The sO2 of each vessel is overlaid on structural en face images. (d)- (f): Fundus images. (g)- (i): Doppler OCT images around the optic disc show opposite flow directions between arteries and veins.


4) Pi, Shaohua, Acner Camino, Miao Zhang, William Cepurna, Gangjun Liu, David Huang, John Morrison, and Yali Jia. "Angiographic and structural imaging using high axial resolution fiber-based visible-light OCT." Biomedical optics express 8, no. 10 (2017): 4595-4608.

The PI's first vis-OCT paper

Fig. 1 (A) Schematic of the visible light optical coherence tomography (vis-OCT) system for rat retina imaging. L1, L2: Lens. (B) Calibrated spectrum in spectrometer using a Neon calibration light source. The center wavelength is 560 nm and full maximum at half width (FWHM) bandwidth is 90 nm. (C) Maximum sensitivity was 89 dB considering the light passes a neutral density (ND) filter (OD = 3.0) twice. Inset shows the measured axial resolution 1.7 μm in air, which is equivalent to 1.2 μm in tissue.

Fig. 2 3.2 × 3.2-mm rat retinal en face angiograms of the (A) superficial vascular plexus (SVP), (B) intermediate capillary plexus (ICP), (C) deep capillary plexus (DCP), and (D) choriocapillaris (CC). scale bar = 200 μm.

Prior OCT

3) Pi, Shaohua, Xie Zeng, Nan Zhang, Dengxin Ji, Borui Chen, Haomin Song, Alec Cheney et al. "Dielectric-grating-coupled surface plasmon resonance from the back side of the metal film for ultrasensitive sensing." IEEE Photonics Journal 8, no. 1 (2015): 1-7.


I designed a novel nano-structure which can launch surface plasmon resonance (SPR) modes efficiently from the back side of metal film, can excite the SPR under the normal incident light, demonstrated very narrow (~4 nm) resonance line width, and showed ultra-wide spectral tunability.

2) Wang, Bingjie, Shaohua Pi, Qi Sun, and Bo Jia. "Improved wavelet packet classification algorithm for vibrational intrusions in distributed fiber-optic monitoring systems." Optical Engineering 54, no. 5 (2015): 055104.

Machine Learning

I assisted to develop an intrusion classification algorithm based on wavelet packet transform, Shannon entropy and neural network.

1) Pi, Shaohua, Bingjie Wang, Bo Jia, Qi Sun, Qian Xiao, and Dong Zhao. "Intrusion localization algorithm based on linear spectrum in distributed Sagnac optical fiber sensing system." Optical Engineering 54, no. 8 (2015): 085105.

Optical Sensing

I developed a Sagnac-based optical fiber sensing system and a "twice-FFT" algorithm to detect and localize vibrational intrusions along a pipeline in real-time.

0) Li, Honglei, Pi Shaohua, and Zhang Qun. "Exploring the stability of threshold voltage for W adopted IZO Thin Film Transistor (IZO: W TFT)." Fudan's Undergraduate Research Opportunities Program, (2010-2011)

Thin Film Transistor (TFT)

I fabricated the IZO: W TFT with magnetron sputtering at different oxygen partial pressure, and measured its electric and optical characterization with step profiler, SEM and spectrophotometer.