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Hyperspectral Imaging (HSI) for fluorescence-guided brain tumor resection enables visualization of differences between tissues that are not distinguishable to humans. This augmentation can maximize brain tumor resection, improving patient outcomes. However, much of the processing in HSI uses simplified linear methods that are unable to capture the non-linear, wavelength-dependent phenomena that must be modeled for accurate recovery of fluorophore abundances. We therefore propose two deep learning models for correction and unmixing, which can account for the nonlinear effects and produce more accurate estimates of abundances. Both models use an autoencoder-like architecture to process the captured spectra. One is trained with protoporphyrin IX (PpIX) concentration labels. The other undergoes semi-supervised training, first learning hyperspectral unmixing self-supervised and then learning to correct fluorescence emission spectra for heterogeneous optical and geometric properties using a reference white-light reflectance spectrum in a few-shot manner. The models were evaluated against phantom and pig brain data with known PpIX concentration; the supervised model achieved Pearson correlation coefficients (R values) between the known and computed PpIX concentrations of 0.997 and 0.990, respectively, whereas the classical approach achieved only 0.93 and 0.82. The semi-supervised approach's R values were 0.98 and 0.91, respectively. On human data, the semi-supervised model gives qualitatively more realistic results than the classical method, better removing bright spots of specular reflectance and reducing the variance in PpIX abundance over biopsies that should be relatively homogeneous. These results show promise for using deep learning to improve HSI in fluorescence-guided neurosurgery., Comment: 20 pages, 8 figures, 3 tables - Under Review

Through spectral unmixing, hyperspectral imaging (HSI) in fluorescence-guided brain tumor surgery has enabled detection and classification of tumor regions invisible to the human eye. Prior unmixing work has focused on determining a minimal set of viable fluorophore spectra known to be present in the brain and effectively reconstructing human data without overfitting. With these endmembers, non-negative least squares regression (NNLS) was used to compute the abundances. However, HSI images are heterogeneous, so one small set of endmember spectra may not fit all pixels well. Additionally, NNLS is the maximum likelihood estimator only if the measurement is normally distributed, and it does not enforce sparsity, which leads to overfitting and unphysical results. Here, we analyzed 555666 HSI fluorescence spectra from 891 ex vivo measurements of patients with brain tumors to show that a Poisson distribution models the measured data 82% better than a Gaussian in terms of the Kullback-Leibler divergence and that the endmember abundance vectors are sparse. With this knowledge, we introduce (1) a library of 9 endmember spectra, (2) a sparse, non-negative Poisson regression algorithm to perform physics-informed unmixing with this library without overfitting, and (3) a highly realistic spectral measurement simulation with known endmember abundances. The new unmixing method was then tested on the human and simulated data and compared to four other candidate methods. It outperforms previous methods with 25% lower error in the computed abundances on the simulated data than NNLS, lower reconstruction error on human data, beUer sparsity, and 31 times faster runtime than state-of-the-art Poisson regression. This method and library of endmember spectra can enable more accurate spectral unmixing to beUer aid the surgeon during brain tumor resection., Comment: 17 pages, 4 tables, 6 figures; Under review

Complete resection of malignant gliomas is hampered by the difficulty in distinguishing tumor cells at the infiltration zone. Fluorescence guidance with 5-ALA assists in reaching this goal. Using hyperspectral imaging, previous work characterized five fluorophores' emission spectra in most human brain tumors. In this paper, the effectiveness of these five spectra was explored for different tumor and tissue classification tasks in 184 patients (891 hyperspectral measurements) harboring low- (n=30) and high-grade gliomas (n=115), non-glial primary brain tumors (n=19), radiation necrosis (n=2), miscellaneous (n=10) and metastases (n=8). Four machine learning models were trained to classify tumor type, grade, glioma margins and IDH mutation. Using random forests and multi-layer perceptrons, the classifiers achieved average test accuracies of 74-82%, 79%, 81%, and 93% respectively. All five fluorophore abundances varied between tumor margin types and tumor grades (p < 0.01). For tissue type, at least four of the five fluorophore abundances were found to be significantly different (p < 0.01) between all classes. These results demonstrate the fluorophores' differing abundances in different tissue classes, as well as the value of the five fluorophores as potential optical biomarkers, opening new opportunities for intraoperative classification systems in fluorescence-guided neurosurgery., Comment: 22 pages, 8 figures

Exoplanets are abundant in our galaxy and yet characterizing them remains a technical challenge. Solar System planets provide an opportunity to test the practical limitations of exoplanet observations with high signal-to-noise data that we cannot access for exoplanets. However, data on Solar System planets differ from exoplanets in that Solar System planets are spatially resolved while exoplanets are unresolved point-sources. We present a novel instrument designed to observe Solar System planets as though they are exoplanets, the Planet as Exoplanet Analog Spectrograph (PEAS). PEAS consists of a dedicated 0.5-m telescope and off-the-shelf optics, located at Lick Observatory. PEAS uses an integrating sphere to disk-integrate light from the Solar System planets, producing spatially mixed light more similar to the spectra we can obtain from exoplanets. This paper describes the general system design and early results of the PEAS instrument., Comment: SPIE Astronomical Telescopes & Instrumentation 2020 Proceedings (11447-153), 9 pages, 9 figures