Publications

2024

• Evaluation of Cellpose segmentation with sequential thresholding for instance segmentation of cytoplasms within autofluorescence images, Nianchao Wang, Linghao Hu, Alex J. Walsh. Computers in Biology and Medicine, 2024. 179:108846.
• Comparison of polystyrene and hydrogel microcarriers for optical imaging of adherent cells, Oscar R. Benavides, Berkley P. White, Holly C. Gibbs, Roland Kaunas, Carl A. Gregory, Kristen C. Maitland, Alex J. Walsh. Journal of Biomedical Optics. 2024. 29(S2):S22708.
• 3D convolutional neural networks predict cellular metabolic pathway use from fluorescence lifetime decay data, Linghao Hu, Daniela De Hoyos, Yuanjiu Lei, A. Phillip West, Alex J. Walsh. APL Bioengineering, 2024. 8, 016112.
  • Featured by AIP Publishing with Scilight Article: Identifying cellular metabolic pathways with label-free imaging and neural networks
• Autofluorescence is a biomarker of neural stem cell activation state, Christopher S. Morrow, Kelsey Tweed, Sabina Farhadova, Alex J. Walsh, Bo P. Lear, Avtar Roopra, Ryan D. Risgaard, Payton C. Klosa, Zachary P. Arndt, Ella R. Peterson, Michelle M. Chi, Allison G. Harris, Melissa C. Skala, Darcie L. Moore, Cell Stem Cell, 2024.

2023

• Label-free spatially maintained measurements of metabolic phenotypes in cells, Linghao Hu, Nianchao Wang, Joshua D. Bryant, Lin Liu, Linglin Xie, A. Phillip West, Alex J. Walsh, Frontiers in Bioengineering and Biotechnology, 2023. 11.
• Perfusability and immunogenicity of implantable pre-vascularized tissues recapitulating features of native capillary network, Dhavan Sharma, Archita Sharma, Linghao Hu, Te-An Chen, Sarah Voon, Kayla J. Bayless, Jeremy Goldman, Alex J Walsh, Feng Zhao, Bioactive Materials, 2023. 30:184-199.
• Comparison of phasor analysis and biexponential decay curve fitting of autofluorescence lifetime imaging data for machine learning prediction of cellular phenotypes, Linghao Hu*, Blanche ter Hofstede*, Dhavan Sharma, Feng Zhao, Alex J Walsh, Frontiers in Bioinformatics, (3), 2023. *Linghao and Blanche contributed equally and share first authorship.
• Evolution of cisplatin resistance through coordinated metabolic reprogramming of the cellular reductive state, Yu, W., Y. Chen, N. Putluri, A. Osman, C. Coarfa, V. Putluri, A. H. M. Kamal, J. K. Asmussen, P. Katsonis, J. N. Myers, S. Y. Lai, W. Lu, C. C. Stephan, R. T. Powell, F. M. Johnson, H. D. Skinner, J. Kazi, K. M. Ahmed, L. Hu, A. Threet, M. D. Meyer, J. A. Bankson, T. Wang, J. Davis, K. R. Parker, M. A. Harris, M. L. Baek, G. V. Echeverria, X. Qi, J. Wang, A. I. Frederick, A. J. Walsh, O. Lichtarge, M. J. Frederick and V. C. Sandulache, British Journal of Cancer, 2023.
• POSEA: A novel algorithm to evaluate the performance of multi-object instance image segmentation, Nianchao Wang, Linghao Hu, Alex J Walsh, PlosOne 18(3): e0283692.=, 2023.
• Volumetric imaging of human mesenchymal stem cells (hMSCs) for non-destructive quantification of 3D cell culture growth, Oscar R Benavides, Holly C Gibbs, BP White, Roland Kaunas, Carl A Gregory, Alex J Walsh, Kristen C Maitland, PlosOne. 2023. 18(3): e0282298.

2022

• Label-free optical imaging of cell function and collagen structure for cell-based therapies, Linghao Hu, Samantha Morganti, Uyen Nguyen, Oscar Benavides, Alex J Walsh, Current Opinion in Biomedical Engineering, 2022.
• Imaging in Scaffolds, Jocelyn Martinez, Nianchao Wang, Linghao Hu, Elizabeth Cardona, Uyen Nguyen, Ricky Martinez, Alex J Walsh. Biomaterial-Based Approaches to Study the Tumour Microenvironment, Royal Chemical Society, Editors: Jessica O. Winter, Shreyas S. Rao. 2022.
• Osr1 regulates macrophage-mediated liver inflammation in non-alcoholic fatty liver disease progression, Liu L, Liu Z, Zhou Y, Li J, Hu Linghao, He L, Gao G, Kidd B, Alex J Walsh, Jiang R, Wu C, Zhang K, Xie L, Cellular and Molecular Gastroenterology and Hepatology, 2022, 15(5) 1117-1133.
• Decellularized organ biomatrices facilitate quantifiable in vitro 3D cancer metastasis models, Sabrina N. VandenHeuvel, Heather A. Farris, Dillon A. Noltensmeyer, Sanjana Roy, Del A. Donehoo, Scott Kopetz, Svasti Haricharan, Alex J. Walsh and Shreya Raghavan. Soft Matter, 2022.
• Design and Implementation of Privilege for Sale, a JEDI Activity for a Biomedical Engineering Introductory Course, Alex J. Walsh, Shreya Raghavan, Biomedical Engineering Education, 2022.
• In vivo fluorescence lifetime imaging of macrophage intracellular metabolism during wound responses in zebrafish. Veronika Miskolci, Kelsey E Tweed, Michael R Lasarev, Emily C Britt, Alex J Walsh, Landon J Zimmerman, Courtney E McDougal, Mark R Cronan, Jing Fan, John-Demian Sauer, Melissa C Skala, Anna Huttenlocher. eLife, 2022, 11:e66080.
• Identification of rare cell populations in autofluorescence lifetime image data. Elizabeth Cardona, Alex J. Walsh, Cytometry Part A, 2022.

2021

• Autofluorescence Imaging to Evaluate Cellular Metabolism. Anna Theodossiou, Linghao Hu, Nianchao Wang, Uyen Nguyen, Alex J. Walsh, J. Vis. Exp. (177), e63282.
• Extracellular pH affects the fluorescence lifetimes of metabolic co-factors. Rebecca Schmitz, Kelsey Tweed, Christine Walsh, Alex J. Walsh*, Melissa C. Skala*. Journal of Biomedical Optics, 2021, 26(5), 056502.
• Carbomer-based adjuvants enhance cross-presentation via metabolic quiescence and lipid body formation Lee W, Kingstad-Bakke B, Paulson B, Larsen A, Marinaik CB, Dulli K, Toy R , Vogel G, Mueller KP, Tweed K, Overmyer K, Walsh AJ, Russell J, Saha K , Reyes L, Skala MC, Sauer JD , Shayakhmetov D, Coon J , Roy K, Suresh M. Plos Pathogens 2021, 17(1): e1009168

2020

• Fluorescence intensity and lifetime redox ratios detect metabolic perturbations in T cells. Hu L, Wang N, Cardona E, and Walsh AJ, Biomedical Optics Express, 2020 (11)10: 5674-5688.
• Classification of T-cell activation via autofluorescence lifetime imaging. Walsh AJ*, Mueller KP, Tweed K, Jones I, Walsh CM, Piscopo NJ, Niemi NM, Pagliarini DJ, Saha K, Skala MC*, Nature Biomedical Engineering, 2020.
  • Behind the Paper Blog Post: Label-free Imaging of T cell Activation, Walsh AJ, Skala MC.

2011-2019

• Classifying T cell activity in autofluorescence intensity images with convolutional neural networks. Wang ZJ, Walsh AJ, Skala MC, Gitter A, Journal of Biophotonics, 2019; e201960050.
• Mutant KRAS exosomes alter the metabolic state of recipient colonic epithelial cells. Zhang Q, Jeppesen DK, Higginbotham JN, Demory Beckler M, Poulin EJ, Walsh AJ, Skala MC, McKinley ET, Manning HC, Hight MR, Schulte ML, Watt KR, Ayers GD, Wolf MM, Andrejeva G, Rathmell JC, Franklin JL, Coffey RJ, Cellular and Molecular Gastroenterology and Hepatology, 2018.
• Optical Metabolic Imaging of Tumor Cell-Cycle Status. Heaster, TM, Walsh AJ, Zhao Y, Hiebert SW, Skala MC, Journal of Biophotonics, 2018; 11(1).
• Functional Optical Imaging of Primary Human Tumor Organoids: Development of a Personalized Drug Screen. Walsh AJ, Cook RS, Skala MC, Journal of Nuclear Medicine, 2017; 59(9) 1367-1372.
• Action potential block in neurons by infrared light. Walsh AJ, Tolstykh GP, Martens S, Ibey BL, Beier HT, Neurophotonics, 2016; 3(4):040501.
• Temporal Binning of Time-Correlated Single Photon Counting Data Improves Exponential Decay Fits and Imaging Speed. Walsh AJ, Sharick JT, Skala MC, Beier HT, Biomedical Optics Express, 2016; 7(4): 1385-1399.
• Optical imaging of drug-induced metabolism changes in murine and human pancreatic cancer organoids reveals heterogeneous drug response. Walsh AJ, Castellanos J, Nagathihalli N, Merchant N, Skala MC, Pancreas, 2016; 45(6): 863-869.
• Drug response in organoids generated from frozen primary tumor tissues. Walsh AJ, Cook RS, Sanders ME, Arteaga CL, Skala MC, Scientific Reports, 2016;6: 18889. 
• In vivo Autofluorescence Imaging of Tumor Heterogeneity in Response to Treatment. Shah AT, Diggins KE, Walsh AJ, Irish JM, Skala MC, Neoplasia, 2015,17(12): 862-870.
• Deconvolution of Fluorescence Lifetime Imaging Microscopy by a Library of Exponentials. Campos-Delago DU, Gutierrez-Navarro O, Arce-Santana ER, Skala MC, Walsh AJ, Jo JA. Optics Express, 2015; 23(18): 23748-67.
• Blind Deconvolution Estimation of Fluorescence Measurements Through Quadratic Programming. Campos-Delago D, Gutierrez-Navarro O, Arce-Santana E, Skala MC, Walsh AJ, Jo J. J Biomedical Optics, 2015; 20(7): 075010.
• STAT3 Mediated Remodeling of the Tumor Microenvironment Results in Enhanced Tumor Drug Delivery in a Mouse Model of Pancreatic Cancer. Nagathihalli NS, Castellanos JA, Beesetty Y, Shi C, Reyzer ML, Caprioli R, Chen X, Walsh AJ, Skala MC, Moses HL, Merchant NB, Gastroenterology, 2015; 149(7): 1932-1943.
• Collagen density and alignment of responsive and resistant trastuzumab-treated breast cancer xenografts. Walsh AJ, Cook RS, Lee JH, Arteaga CL, Skala MC, Journal of Biomedical Optics, 2015; 20(2): 026004.
• Optical metabolic imaging quantifies heterogeneous cell populations. Walsh AJ, Cook RS, Lee JH, Arteaga CL, Skala MC, Biomedical Optics Express, 2015; 6(2):559-573.
• High-throughput measurements of the optical redox ratio using a commercial microplate reader. Cannon TM, Shah AT, Walsh AJ, Skala MC, Journal of Biomedical Optics, 2015; 20(1):010503.
• Quantitative optical imaging of primary tumor organoid metabolism predicts drug response in breast cancer. Walsh AJ, Cook RS, Sanders ME, Arteaga CL, Skala MC, Cancer Research, 2014; 74(18): 5184-5194.
• In vivo hyperspectral imaging of microvessel response to Herceptin treatment. McCormack DR, Walsh AJ, Sit WW, Chen J, Cook RS, and Skala MC, Biomedical Optics Express, 2014; 5(7): 2247-2261.
• Optical Metabolic Imaging Resolves Treatment Response in Head and Neck Squamous Cell Carcinoma. Shah AT, Demory-Beckler M, Walsh AJ, Pohlmann P, Skala MC, “PLoS ONE, 2014; 9(3): e90746.
• The NADH oxidase ENOX1, a critical mediator of endothelial cell radiosensitization, is crucial for vascular development. Venkateswara A, Sekhar KR, Levic DS, Melville DB, Clark TA, Rybski WM, Walsh AJ, Skala MC,  Crooks PA, Knapik EW, Freeman ML, Cancer Research, 2014; 74(1): 38-43.
• Optical imaging identifies breast cancer glycolytic levels, subtypes, and early treatment response. Walsh AJ, Cook RS, Manning HC, Hicks DJ, Lafontant A, Arteaga CL, Skala MC. Cancer Research. 2013; 73(20):6164-74.
• Quantitative Optical Imaging of Vascular Response in vivo in a Model of Peripheral Arterial Disease. Poole KM, Tucker-Schwartz JM, Sit WW, Walsh AJ, Duvall CL, Skala MC. AJP-Heart and Circulatory Physiology. 2013; 305(8):H1168-80.
• The effects of varying glucose concentrations on cellular glycolytic rates. Givens R, Walsh AJ, Skala MC. Young Scientist. 2013; 3:62-64.
• Ex vivo optical metabolic measurements from culture tissue reflect in vivo tissue status. Walsh AJ, Poole KM, Duvall CL, Skala, MC.   Journal of Biomedical Optics. 2012;17(11):116015.
• The novel antiangiogenic VJ115 inhibits the NADH oxidase ENOX1 and cytoskeleton-remodeling proteins. Venkateswaran A, Friedman DB, Walsh AJ, Skala MC, Sasi S, Rachakonda G, Crooks PA, Freeman ML, Sekhar KR. Investigational New Drugs. 2012: 1-10.
• The effect of temperature on the autofluorescence of scattering and non-scattering tissue. Walsh AJ, Masters DB, Jansen ED, Welch AJ, Mahadevan-Jansen A. Lasers in Surgery and Medicine. 2012; 44(9): 712-8.
• Optical imaging of metabolism in HER2 overexpressing breast cancer cells. Walsh AJ, Cook RS, Rexer B, Arteaga CL, Skala MC. Biomedical Optics Express. 2012;3(1):75-85.
• Development of spectral markers for the discrimination of ulcerative colitis and Crohn’s disease using Raman spectroscopy. Bi X, Walsh A, Mahadevan-Jansen A, Herline A. Diseases of the Colon and Rectum. 2011;54(1):48-53.
• Variation of fluorescence in tissue with temperature. Zaman RT, Rajaram N, Walsh A, Oliver J, Rylander HG, Tunnell JW, Welch AJ, Mahadevan-Jansen A. Lasers in Surgery and Medicine. 2011;43(1):36-42.