Publications

2026

July

De la Cadena A, Aksamitiene E, Boppart SA. Unified Vibrational and Multiphoton Label-Free Nonlinear Microscopy for Simultaneous Chemical and Structural Imaging. IEEE J Sel Top Quantum Electron. 2026 Jul-Aug;32(4):7100612. doi: 10.1109/jstqe.2025.3650148. Epub 2026 Jan 5. PMID: 41809093; PMCID: PMC12971071.

June

Fliflet AM, Spradlin RA, Tan Y, Nishitha Vijayan A, Choi SJ, Kao WC, Aksamitiene E, Nelappana M, Ding S, Huang KY, Joshi A, Kambar N, Bludgen T, Meehan M, Boss JL, Knipp M, Fan H, Leal C, Sunde RA, Dobrucki LW, Boppart SA, Kong HJ, Sweedler JV, Boppart MD. Exercise Training Stimulates the Release of Glutathione Peroxidase 1 (GPX1)-Enriched Extracellular Vesicles That Promote Angiogenesis. FASEB J. 2026 Jun 30;40(12). doi: 10.1096/fj.202505096RR. PMID: 42313915; PMCID: PMC13278521.

García-López-de-Haro C, Fuster-Barceló C, Rueden CT, Heras J, Ulman V, Franco-Barranco D, Inés A, Eliceiri KW, Olivo-Marin JC, Tinevez JY, Sage D, Muñoz-Barrutia A. SAMJ: fast image annotation on ImageJ/Fiji via segment anything model. Nat Commun. 2026 Jun 18;17(1):5402. doi: 10.1038/s41467-026-71752-x. PMID: 42315510; PMCID: PMC13279790.

Meharry SL, Borensztejn A, Gaudreault N, Lucas J, Medrash G, Schaefbauer L, Toloudis D, Wallace A, Whitney B, Wilhelm L, Ben-Simon Y, Burel JM, Chen J, Eliceiri KW, Grüneboom A, Kyoda K, Moore J, Moore W, Onami S, Panzeri D, Rueden CT, Tasic B, Johnson GT. Search, organize, aggregate and share image data with BioFile Finder (BFF). Nat Methods. 2026 Jun 15. doi: 10.1038/s41592-026-03130-w. Epub ahead of print. PMID: 42298069.

Ahn Y, Lee JH, Hurd C, Lee J, Park J, Markowicz AA, Zhang Z, Hwang J, Monroy GL, Rogers SA, Jung W, Boppart SA, Kong H. Microblasting Wound Dressings Mechanically Disrupt Polymicrobial Biofilms to Enhance Healing in Treatment-Resistant Wounds. Adv Sci (Weinh). 2026 Jun 10. doi: 10.1002/advs.75999. Epub ahead of print. PMID: 42267543.

Zhao W, Samimi K, Skala MC, Datta R. FLIM Playground: An interactive, end-to-end graphical user interface for analyzing single cells with fluorescence lifetime imaging microscopy. Cell Rep Methods. 2026 Jun 10:101484. doi: 10.1016/j.crmeth.2026.101484. Epub ahead of print. PMID: 42269617.

Garrett DC, Wang LV. An ingestible light source for deep photoacoustic imaging. Photoacoustics. 2026 Jun 2;50:100844. doi: 10.1016/j.pacs.2026.100844. PMID: 42292766; PMCID: PMC13264102.

Yang Q, Guan Y, Aguilera N, Liu T, Li J, Das V, Attar EC, Krynitsky J, Pursley R, Dubra A, Bower AJ, Tam J. High throughput volumetric retinal imaging of cellular structures using adaptive optics optical coherence tomography at 3 MHz. Invest Ophthalmol Vis Sci. 2026 Jun;67(7):373. ARVO Annual Meeting Abstract.

Guan Y, Yang Q, Aguilera N, Liu T, Das V, Attar EC, Krynitsky J, Pursley R, Li J, Bower AJ, Tam J. Improved visualization of choroidal structures using non-confocal adaptive optics scanning light ophthalmoscopy at 1060 nm. Invest Ophthalmol Vis Sci. 2026 Jun;67(7):371. ARVO Annual Meeting Abstract.

De la Cadena A, Aksamitiene E, Ho RJ, Bhargava R, Boppart SA. Label-free multimodal nonlinear microscopy enabled by an optical parametric generator. APL Photonics. 2026 Jun;11(6):066121. doi: 10.1063/5.0331944. Epub 2026 Jun 18. PMID: 42338573; PMCID: PMC13285749.

Sanchez Z, de Jesus M, David M, Taheri A, Olatunji SY, Rahmoon M, Eliceiri KW, Mahadevan-Jansen A, Millis BA. Remotely accessible optical microscopy education through a wide (and global) lens. J Microsc. 2026 Jun;302(3):406-418. doi: 10.1111/jmi.70112. Epub 2026 May 15. PMID: 42138143.

Pineda Guzman RA, Moghaddam AO, Confer MP, Majumdar S, Bhargava R, Wagoner Johnson AJ, Damon BM, Kersh ME. Non-invasive detection of local microstructural damage in tendon using Diffusion Tensor MRI. Acta Biomater. 2026 Jun;217:326-337. doi: 10.1016/j.actbio.2026.05.012. Epub 2026 May 8. PMID: 42107579.

May

Rout J, Mishra M, Barik RC, Yadav DK, Prasad DK, Sekh AA. Stacked multi-fusion CNN: an adaptive attention model for privacy preserving deepfake forensics. Sci Rep. 2026 May 29. doi: 10.1038/s41598-026-55325-y. Epub ahead of print. PMID: 42215677.

Zhang H, Xu X, Ta C, Zurutuza I, Gautam KS, Hongsermeier C, Blasi N, Voorugonda S, Mukherjee-Roy N, Gao J, Sumer B, Akers WJ, Achilefu S. Bridging preclinical and clinical fluorescence-guided surgery with advanced cancer vision goggles. Npj Imaging. 2026 May 25;4(1):36. doi: 10.1038/s44303-026-00170-x. PMID: 42185570; PMCID: PMC13201569.

• Udgata S, Schmitz AE, Gillette AA, Sorenson AG, Riendeau JM, Engeldinger R, Stoecker JN, Steimle AK, Johnson KA, Kittelson D, Isaak A, Kratz JD, Carchman E, Kimple R, Pasch CA, Skala MC, Deming DA. Organoid Level Assessments of Human Primary and Metastatic Colorectal Cancer-Derived Organoids Predict Response to Chemotherapy and Chemoradiation. Cancers (Basel). 2026 May 13;18(10):1587. doi: 10.3390/cancers18101587. PMID: 42192947; PMCID: PMC13205027.

Cohen S, Shamai G, Sabo E, Cretu A, Barshack I, Goldman T, Bar-Sela G, Pearson AT, Huo D, Howard FM, Kimmel R, Mayer C. Prediction of OncotypeDX recurrence score using hematoxylin and eosin-stained whole slide images. NPJ Breast Cancer. 2026 May 11. doi: 10.1038/s41523-026-00937-w. Epub ahead of print. PMID: 42115215.

Howard FM, Li A, Kochanny S, Sullivan M, Flores EM, Dolezal J, Khramtsova G, Jain-Liu S, Medenwald R, Saha P, Fan C, McCart L, Watson M, Teras LR, Bodelon C, Patel A, Symmans WF, Partridge AH, Carey L, Olopade OI, Stover D, Perou C, Yao K, Pearson AT, Huo D. Histology-Derived Signatures Predict Recurrence Risk and Chemotherapy Benefit in Randomized Trials of Early Breast Cancer. medRxiv [Preprint]. 2026 May 5:2026.04.23.26351499. doi: 10.64898/2026.04.23.26351499. PMID: 42078387; PMCID: PMC13131706.

Lee YJ, Eom TJ, Wang LV. Frequency-domain photoacoustic microscopy with resonant transducer and interferometric modulation for high-reliability sO2 imaging. Photoacoustics. 2026 May 1;49:100834. doi: 10.1016/j.pacs.2026.100834. PMID: 42111354; PMCID: PMC13156710.

Cao H, Spitz S, Yu LY, Liu K, Zhang Z, Presutti F, Pramotton FM, Kulkarni S, Kamm RD, You S. Self-localized ultrafast pencil beam for volumetric multiphoton imaging. Nat Methods. 2026 May;23(5):1024-1036. doi: 10.1038/s41592-026-03067-0. Epub 2026 Apr 27. PMID: 42045469.

Luo X, Cao R, Hu P, Luo Y, Zeng Y, Zhang Y, Cui M, Zhou Q, Ku G, Wang LV. Multifocal Optical-Resolution Photoacoustic Microscopy With a Masked Single-Element Transducer. IEEE Trans Med Imaging. 2026 May;45(5):2015-2022. doi: 10.1109/TMI.2025.3643618. PMID: 41385414; PMCID: PMC13056231.

Basumatary J, Aborahama Y, Zhang Y, Zhang Y, Zeng Y, Liu CZ, Zhou Q, Wang LV. High-Speed Volumetric Dual-Mode Ultrasound and Photoacoustic Tomography With a Single-Element Detector. IEEE Trans Med Imaging. 2026 May;45(5):2317-2328. doi: 10.1109/TMI.2026.3653667. PMID: 41525532; PMCID: PMC13189059.

April

Spezia MC, Dy CJ, Farrell B, Iftikhar A, DeMartini S, Perez R, Achilefu S, Brogan DM. Near infrared fluorophore specific for annexin A2 identifies peripheral nerve injury in a rodent transection model. Front Cell Dev Biol. 2026 Apr 29;14:1657209. doi: 10.3389/fcell.2026.1657209. PMID: 42137368; PMCID: PMC13168058.

Garrett DC, Xu J, Oh D, Aborahama Y, Ku G, Maslov K, Tseng WW, Wang LV. Whole cross-sectional human ultrasound tomography. Nat Biomed Eng. 2026 Apr 24. doi: 10.1038/s41551-026-01660-4. Epub ahead of print. PMID: 42032040.

Reed-McBain CA, Anchan AS, Patel JD, Peterson EP, Gómez García I, Riendeau J, Chavira C, Hua NW, Choi A, Saperstein JR, Drew TJ, Banks MI, Skala M, Ayuso JM. Microfluidic device to study spatial and temporal response of astrocyte networks in response to changes in the biochemical milieu. Microsyst Nanoeng. 2026 Apr 23;12:150. doi: 10.1038/s41378-026-01213-4. PMID: 42026032; PMCID: PMC13106794.

Gillette AA, Hsu A, Udgata S, Schmitz A, Deming DA, Skala M. Rapid assessment of patient derived cancer organoids using label-free imaging and an automated analysis pipeline [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res. 2026 Apr;86(7 Suppl) nr 2617. doi: 10.1158/1538-7445.AM2026-2617.

Lee JH, Ahn Y, Markowicz AA, Monroy GL, Hurd C, Lee J, Park J, Park EJ, Rogers SA, Boppart SA, Kong H. Surface versus Nanocatalyst-Induced Matrix Bubbles Govern Temperature-Dependent Biofilm Removal. ACS Appl Mater Interfaces. 2026 Apr 15;18(14):20058-20072. doi: 10.1021/acsami.6c00615. Epub 2026 Mar 31. PMID: 41914507; PMCID: PMC13186288.

Das B, Prasad DK, Sekh AA. IReCAPTCHA: a robust image-reasoning CAPTCHA system. Cybersecur (Singap). 2026;9(1):54. doi: 10.1186/s42400-025-00484-0. Epub 2026 Apr 13. PMID: 41982340; PMCID: PMC13070986.

Lu C, Sengupta S, Li H, Anastasio MA. Observer-usable Information as a Task-specific Image Quality Metric. IEEE Trans Med Imaging. 2026 Apr 7;PP. doi: 10.1109/TMI.2026.3680092. Epub ahead of print. PMID: 41945813.

Shamai G, Cohen S, Binenbaum Y, Sabo E, Cretu A, Mayer C, Barshack I, Goldman T, Bar-Sela G, Polónia A, Huo D, Pearson AT, Howard FM, Sparano JA, Kimmel R, Aran D. Deep learning on histopathological images to predict breast cancer recurrence risk and chemotherapy benefit: a multicentre, model development and validation study. Lancet Oncol. 2026 Apr;27(4):512-526. doi: 10.1016/S1470-2045(25)00727-2. Epub 2026 Mar 11. PMID: 41831466; PMCID: PMC12989675.

Delos Santos S, Invernizzi M, Liu C, Tong X, Rosen J, Wang LV, Lai LL. Utilizing post-imaging surveys to guide development of photoacoustic computed technology for breast imaging. Am J Surg. 2026 Apr;254:116828. doi: 10.1016/j.amjsurg.2026.116828. Epub 2026 Jan 17. PMID: 41576593; PMCID: PMC12862834.

March

Lee Y, Nickel KP, Kiernan MJ, Al Mukaddim R, Liu Y, Mitchell V, Ngawang T, Salamat S, Wilbrand SM, Graham M, Eliceiri KW, Kimple RJ, Dempsey RJ, Varghese T. Introducing ARONG, A 3D Reconstruction Method for Highly Deformed Histology. J Imaging Inform Med. 2026 Mar 31. doi: 10.1007/s10278-026-01905-3. Epub ahead of print. PMID: 41917246.

Wilson HM, V Chacko J, Odde DJ, Provenzano PP, Eliceiri KW. FLIM quality metric visualization as a means to validate consistency across large-area non-homogeneous FLIM datasets. Methods Appl Fluoresc. 2026 Mar 18;14(2):025004. doi: 10.1088/2050-6120/ae4e7b. PMID: 41791226; PMCID: PMC13169974.

Ma H, Zhang C, Zheng S, Chen S, Liu Y. Automated Cyclic Super-Resolution Microscopy for Nanoscale Protein Mapping. bioRxiv [Preprint]. 2026 Mar 17:2026.03.16.712232. doi: 10.64898/2026.03.16.712232. PMID: 41889909; PMCID: PMC13015466.

Xu X, Zhang H, Ta C, Zurutuza I, Blasi N, Gautam KS, Hongsermeier C, Trivedi V, Jovan J, Nussinov Z, Seidel A, Li F, Shen M, Leu W, Hite H, Dunn J, Buras W, Gao J, Sumer B, Akers WJ, Achilefu S. Single-Operator Cancer Vision Goggles for Quantitative Near-Infrared Fluorescence-Guided Oncologic Surgery. IEEE Trans Biomed Eng. 2026 Mar 12;PP:10.1109/TBME.2026.3673650. doi: 10.1109/TBME.2026.3673650. Epub ahead of print. PMID: 41818009; PMCID: PMC13295128.

Riendeau J, Hockerman L, Maly E, Samimi K, Skala M. Autofluorescence lifetime imaging resolves cell heterogeneity within peripheral blood mononuclear cells. bioRxiv [Preprint]. 2026 Mar 8:2026.03.06.710224. doi: 10.64898/2026.03.06.710224. PMID: 41867750; PMCID: PMC13001478.

Li M, Yuan Y, Ding G, Ni H, Gao B, Dong D, He Q, He H, Teng X, Sun Y, Sun D, Xia Q, Pham T, Cheng JX. Mid-wave infrared photothermal microscopy for molecular and metabolic imaging in deep tissues and spheroids. arXiv [Preprint]. 2026 Mar 6. Available from: https://arxiv.org/abs/2603.05785

Burchett Darantiere A, Zarodniuk M, Giza S, Rexroat J, Kuehl P, Clements T, Balraj K, Najera J, Bhargava R, Datta M. Multi-omics and spatial analysis of microgravity-grown glioblastoma organoids reveals superior modeling of advanced disease after long-term spaceflight. bioRxiv [Preprint]. 2026 Mar 6:2026.03.06.710192. doi:10.64898/2026.03.06.710192.

Alfaro R, Matt A, Liang H, Wang P, Hong G, Zhou C. Optical clearing with absorbing dyes enables non-invasive OCT characterization of adipose tissue subtypes in vivo. Proc SPIE. 2026 Mar 6;PC13837:PC1383716. doi:10.1117/12.3083069.

Zhou M, Dong B, Lukov L, Ma S, He X, Zafarjafarzadeh N, Zhang C. Interface-Sensitive Epi-Coherent Anti-Stokes Raman Scattering Microscopy for Imaging Cell Adhesion Dynamics. Anal Chem. 2026 Mar 5. doi: 10.1021/acs.analchem.5c06485. Epub ahead of print. PMID: 41784803.

Tang R, Yin J, Weinberg B, Lin H, Lu J, Gate D, Klementieva O, Cheng JX. Mid-infrared photothermal mesoscope with millimeter field of view and sub-micron spatial resolution. Proc SPIE. 2026 Mar 5;13864:1386405. doi:10.1117/12.3079290

Qin Y, Agarwal K. 3D refractive index imaging from coherent label-free microscopy: inverse scattering reconstruction and the influence of illumination modes. Proc SPIE. 2026 Mar 5;13861:138610E. doi:10.1117/12.3079110.

Alfauri H, Hao S, Hua H, Rajagopal R, Zhou C. NeuroVisionTrack: in vivo quantification of ocular motor function and visual acuity via OCT-based retina tracking. Proc SPIE. 2026 Mar 5;PC13831:PC138310I. doi:10.1117/12.3085311.

Ren C, Zhang S, Hao S, Song A, Liang H, Xue J, Rajagopal R, Zhou C. Complementary evaluation of impaired retinovascular hemo-functionalities in diabetic mice model with dual waveband OCT in vivo. Proc SPIE. 2026 Mar 5;PC13831:PC1383107. doi:10.1117/12.3085578.

Adkins AJ, Hao S, Hossain AR, Paul R, Bocsi D, Zhou C. Simultaneous dual-eye optical coherence tomography with a head-mounted wearable device. Proc SPIE. 2026 Mar 5;PC13831:PC138310U. doi:10.1117/12.3084544.

Ahmadi F, Sun S, Zhao J, Chen J, Wilson MB, Damon B, Wu Y, Almpani K, Chung R, Jani P, Chen P, Slate EH, Lee JS, Sagl B, Yao H. A Computational Framework for Simulating Patient-Specific TMJ Biomechanics Using a Combined Multibody Dynamics and Finite Element Approach. Ann Biomed Eng. 2026 Mar 2. doi: 10.1007/s10439-026-04020-0. Epub ahead of print. PMID: 41770438.

Zhu Y, Ni H, He H, Li Y, Zhang M, Cheng JX. Single-pulse stimulated Raman photothermal microscopy and direct visualization of cholesterol-rich membrane domains. arXiv [Preprint]. 2026 Mar 2. Available from: https://arxiv.org/abs/2603.01386

Hu P, Tong X, Lin L, Wang LV. Data-Driven System Matrix Manipulation Enabling Fast Functional Imaging in Tomography. IEEE Trans Med Imaging. 2026 Mar;45(3):906-918. doi: 10.1109/TMI.2025.3612437. PMID: 40982496; PMCID: PMC12772519.

Butola A, Ghosh B, Park J, Kwon M, De la Cadena A, Mukherjee SS, Bhargava R, Boppart SA, Agarwal K. Label-free correlative morpho-chemical tomography of 3D kidney mesangial cells. J Biomed Opt. 2026 Mar;31(3):036501. doi: 10.1117/1.JBO.31.3.036501. Epub 2026 Mar 10. PMID: 41816704; PMCID: PMC12972753.

Kerschner JE, Daley RA Jr, Link R, Jones RM, Peterson KJ, Chun RH, Flanary VA, Gorelik M, Keppel KL, Maksimoski M, Malloy M, Martin TJ, McCormick ME, Robey TC, Ansari S, Matoska GM, Rupcich CA, Saunderson ML, Shay SG, Sulman C, Erbe C, Thompson JK, Khampang P, Yan K, Simpson PM, Ho A, Monroy GL, Spillman DR, Aksamitiene E, Boppart SA. Clinical trial assessing the use of optical coherence tomography in decision making for children presenting with acute otitis media. Int J Pediatr Otorhinolaryngol. 2026 Mar;202:112728. doi: 10.1016/j.ijporl.2026.112728. Epub 2026 Jan 14. PMID: 41547297; PMCID: PMC13019881.

Brooks FJ, Anastasio MA. A Taxonomy of Machine Hallucination in Radiology. Radiol Artif Intell. 2026 Mar;8(2). doi: 10.1148/ryai.250203. PMID: 41811081; PMCID: PMC13019329.

Garrett DC, Aborahama Y, Xu J, Ku G, Wang LV. Microwave Ablation Monitoring Using Thermoacoustic and Ultrasound Tomography. IEEE J Microw. 2026 Mar;6(2):531-539. doi: 10.1109/jmw.2025.3612329. Epub 2025 Oct 10. PMID: 42078006; PMCID: PMC13132507.

February

Hahm ER, Jacobs BL, Singh KB, Kim SH, Parikh R, Normolle DP, Dhir R, Oyebamiji T, Sun X, Liu Y, Appleman LJ, Gelhaus SL, Singh SV. Bench-to-Bedside Evaluation of Sulforaphane/BroccoMax® on Fatty Acid Synthesis in Prostate Cancer. Cancer Prev Res (Phila). 2026 Feb 25:10.1158/1940-6207.CAPR-25-0488. doi: 10.1158/1940-6207.CAPR-25-0488. Epub ahead of print. PMID: 41738426; PMCID: PMC13034680.

Tan KKD, Condon AM, Renteria CA, Iyer RR, Ho A, Shi J, Sorrells JE, Aksamitiene E, Usselman RJ, Boppart SA. Investigating Cellular Magnetic Bioeffects Using Two-Channel, Two-Photon Autofluorescence Lifetime Microscopy. IEEE Trans Mol Biol Multiscale Commun. 2026;12:398-406. doi: 10.1109/tmbmc.2026.3666858. Epub 2026 Feb 23. PMID: 41908264; PMCID: PMC13026082.

Floryan M, Cordiale A, Jensen H, Chen J, Guo Z, Vinayak V, Kheiri S, Raman R, Shenoy V, Cambria E, Kamm R. IntravChip: a vascularized and perfused microfluidic model of the primary tumor microenvironment to collect intravasated tumor cells. bioRxiv [Preprint]. 2026 Feb 20:2026.02.19.706805. doi: 10.64898/2026.02.19.706805. PMID: 41757054; PMCID: PMC12934641.

Pham DL, Kalluri M, Weaver C, Hsu A, Gillette A, Zhao W, Kearl T, Hematti P, Shah NN, Skala MC. Autofluorescence imaging reveals the impact of cryopreservation on T cell metabolism and activation response. Mol Ther Adv. 2026 Feb 19;34(2):201704. doi: 10.1016/j.omta.2026.201704. PMID: 42137595; PMCID: PMC13148902.

Liu N, Shiravi S, Jin T, Liu J, Zhu Z, Li J, Cheung I, Zhang H, Wang Y, Li Q, Xu Z, Zeng L, Quezada MJ, Villalobos A, Samei Y, Khanna S, Bao S, Wu M, Liang S, Cheng X, Lv Z, Maeng WY, Zhang Y, Luan H, Boppart SA, Huang Y, Zhang Y, Franz CK, Finan JD, Rogers JA. Shape-conformal porous frameworks for full coverage of neural organoids and high-resolution electrophysiology. Nat Biomed Eng. 2026 Feb 18. doi: 10.1038/s41551-026-01620-y. Epub ahead of print. PMID: 41708937.

Hsu A, Samimi K, Gillette AA, Udgata S, Schmitz AE, Zhao W, Deming DA, Skala MC. An automated image analysis pipeline for wide-field optical redox imaging of patient-derived cancer organoids. Sci Rep. 2026 Feb 18;16(1):9757. doi: 10.1038/s41598-026-40249-4. PMID: 41708789; PMCID: PMC13013648.

Chen HP, Ngo TKN, Mao BH, Jang H, Shin SC, Kamm R, Chung S, Tu TY. Matrix-matrix interfaces orchestrate early mechanosensitive transition from attractor to track. BioChip J. 2026 Feb 16;20:339-355. doi: 10.1007/s13206-026-00219-y.

Arbabi S, Vincent H, Hansen E, Connaughton M, Sovitzky N, Haugstad G, Falahkheirkhah K, Bhargava R, Dabagh M. Developing virtual physiology of human tumor tissue for malignancy assessment. NPJ Precis Oncol. 2026 Feb 14;10(1):136. doi: 10.1038/s41698-026-01316-1. PMID: 41691055; PMCID: PMC13022302.

Ding G, Sun D, Zhu Y, Tang R, Ni H, Yuan Y, Lin H, Cheng JX. Micromolar chemical imaging by high-energy low-photodamage coherent anti-Stokes Raman scattering (HELP-CARS). arXiv [Preprint]. 2026 Feb 9. Available from: https://arxiv.org/abs/2602.09245

Zhang H, Chen Z, Qian G, Zahm CD, Alonso-Matilla R, Fischer S, Stromnes IM, Webber BR, Eliceiri KW, Odde DJ, Moriarity BS, Provenzano PP. Engineering "physically optimized" T cells for increased sampling of complex tumor microenvironments. bioRxiv [Preprint]. 2026 Feb 1:2026.01.28.702394. doi: 10.64898/2026.01.28.702394. PMID: 41659509; PMCID: PMC12873883.

Singh IK, Dong B, Zafarjafarzadeh N, Zhang C. Crosstalk-Free Real-Time Precision Opto-Control of Biochemical Processes Through Intra-Pixel Optical Decoupling. Chemistry-Methods. 2026 Feb;6(2):e202500153.

Zitnay RG, Alizada S, Moustafa TE, Lange D, Schreiber L, Lex A, Judson-Torres RL, Zangle TA, Belote RL. QUILPEN Provides Independent and Label-Free Single-Cell Quantification of Pigmentation Dynamics and Organelle Content. Pigment Cell Melanoma Res. 2026 Feb;39(2):e70080. doi: 10.1111/pcmr.70080. PMID: 41776748.

January

Punnakkal AR, Jadhav SS, Celeste AV, Horsch A, Agarwal K, Prasad DK. 3D Mitochondria Shape Library for Optical Microscopy (3DMSL): A multimodal dataset for deep learning based mitochondrial analysis. Data Brief. 2026 Jan 29;65:112507. doi: 10.1016/j.dib.2026.112507. PMID: 41704521; PMCID: PMC12907005.

Yang K, Park S, Jeong G, Huang HK, Oraevsky AA, Villa U, Anastasio MA. A Learning-based Framework for Spatial Impulse Response Compensation in 3D Photoacoustic Computed Tomography. ArXiv [Preprint]. 2026 Jan 28:arXiv:2601.20291v1. PMID: 41647217; PMCID: PMC12869413.

Quezada MJ, Lee J, Lv Z, Nandoliya K, Cheung I, Wang Q, Maeng WY, Liu N, Vahabikashi A, Ha KH, Kang YW, Song DH, Huang Y, Asseily C, da Cruz RW, Khanna S, Liu J, Finan JD, Leoni L, Procissi D, Huang Y, Yi GC, Bae J, Rogers JA, Franz CK. Multiscale 3D microfluidic platform for intraorganoid delivery. Res Sq [Preprint]. 2026 Jan 27:rs.3.rs-8436544. doi: 10.21203/rs.3.rs-8436544/v1. PMID: 41646406; PMCID: PMC12869557.

Sorrells JE, Yang L, Iyer RR, Zaki FR, Markowicz AA, Monroy GL, Aksamitiene E, Marjanovic M, Boppart SA. Real-time, high-resolution metabolic characterization of live bacteria using label-free optical metabolic imaging. NPJ Biofilms Microbiomes. 2026 Jan 27;12(1):55. doi: 10.1038/s41522-026-00920-0. PMID: 41593068; PMCID: PMC12949149.

Chen P, Park S, Jeong G, Cam RM, Villa U, Anastasio MA. Benchmarking Deep Learning-Based Reconstruction Methods for Photoacoustic Computed Tomography with Clinically Relevant Synthetic Datasets. ArXiv [Preprint]. 2026 Jan 23:arXiv:2601.17165v1. PMID: 41647213; PMCID: PMC12869380.

Egbulefu C, Black K, Su X, Karmakar P, Habimana-Griffin L, Sudlow G, Prior J, Onejeme E, Zheleznyak A, Xu B, Xu Y, Esser A, Mixdorf M, Moss E, Manion B, Hongsermeier C, Gamadia N, Blasi N, Stallings L, Alagbaoso C, Reed N, Gubin MM, Lin CY, Schreiber R, Weilbaecher K, Achilefu S. Radionuclide-stimulated dynamic therapy induces complementary immunogenic necroptosis and apoptosis cancer cell death pathways. Commun Biol. 2026 Jan 19;9(1):275. doi: 10.1038/s42003-026-09555-5. PMID: 41554980; PMCID: PMC12916984.

Zhang Y, Na S, Russin JJ, Sastry K, Lin L, Zheng J, Luo Y, Tong X, An Y, Hu P, Maslov K, Tan TW, Liu CY, Wang LV. Rotational ultrasound and photoacoustic tomography of the human body. Nat Biomed Eng. 2026 Jan 16. doi: 10.1038/s41551-025-01603-5. Epub ahead of print. PMID: 41545778. Park B, Cao R, Luo Y, Liu C, Zeng Y, Zhang Y, Zhou Q, Davis S, D'Apuzzo M, Wang LV. Rapid cancer diagnosis using deep learning-powered label-free subcellular-resolution photoacoustic histology. Sci Adv. 2025 Nov 21;11(47):eadz1820. doi: 10.1126/sciadv.adz1820. Epub 2025 Nov 21. PMID: 41270177; PMCID: PMC12637292.

Joshi E, Shi Y, Montillo A, Lewis M, Peshock R, Wang G, Achilefu S. Anatomically constrained liver CT anomaly detection using healthy priors with diffusion-based inpainting. Res Sq [Preprint]. 2026 Jan 16.3.rs-8563123. doi: 10.21203/rs.3.rs-8563123/v1. PMID: 41646318; PMCID: PMC12869632.

Bhargava A, Schmalz L, López-Espina C, Watson G, Updike L, Urdiales D, Khan S, Bashir R, Reddy B. The clinician-artificial intelligence partnership in early sepsis identification: Leveraging predictive intelligence for enhanced financial outcomes. Research Square [Preprint]. 2026 Jan 6. doi:10.21203/rs.3.rs-8483930/v1.

Heaton AR, Burkard NJ, Gao A, Hoefges A, Feils AS, Burkard SK, Felder MA, Tsarovsky NW, Spiegelman DV, Lublin GM, Hampton AA, D'Amato A, Dinh HQ, Rakhmilevich AL, Erbe AK, Sondel PM, Skala MC. Divergent role of CD8 T cells with distinct metabolic phenotypes during curative radio-immunotherapy in hot versus cold tumors. bioRxiv [Preprint]. 2026 Jan 5:2025.10.24.684274. doi: 10.1101/2025.10.24.684274. PMID: 41279819; PMCID: PMC12633444.

Ramasubramanian TS, Adstamongkonkul P, Scribano CM, Johnson C, Caenepeel S, Hrycyniak LCF, Vedder LC, Dana N, Baltes C, Browning V, Chen YI, Dietz T, Flietner E, Kaplewski N, Kellner A, Korrer M, Liu C, Marhefke N, McDonnell P, Nasreen A, Pope V, Prasad A, Richardson J, Schneider S, Schultz MM, Sood C, Sunil A, Euw EV, Wait E, Wargowski EE, Advani P, Broome B, Bruckbauer A, Godwin A, Kokabi N, Lou Y, Martin RCG 2nd, Robaina M, Toia G, Routh J, Friedl A, Eliceiri K, Szulczewski M, Johnson S, Oliner J, Galon J, Capitini C, Mukhopadhyay D, Taube J, Braun D, Gierman HJ. A live tumor fragment platform to assess immunotherapy response in core needle biopsies while addressing challenges of tumor heterogeneity. J Transl Med. 2026 Jan 3;24(1):18. doi: 10.1186/s12967-025-07378-2. PMID: 41484629; PMCID: PMC12763878.

Hale J, Cudworth N, Farrell R, Bhargava A, Eliceiri KW, Rosado-Mendez I. Improved imaging interfaces on a co-registered ultrasound and optical microscopy multiscale system. J Biomed Opt. 2026 Jan;31(1):016002. doi: 10.1117/1.JBO.31.1.016002. Epub 2025 Dec 25. PMID: 41503365; PMCID: PMC12771023.

Fan Z, Lu C, Yue J, Anastasio M, Sun L, Wang X, Li H. Enhancing deep learning interpretability for hand-crafted feature-guided histologic image classification via weak-to-strong generalization. J Med Imaging (Bellingham). 2026 Jan;13(1):017502. doi: 10.1117/1.JMI.13.1.017502. Epub 2026 Jan 20. PMID: 41567872; PMCID: PMC12818695.

Tong X, Liu CZ, Luo Y, Lin L, Dzubnar J, Invernizzi M, Delos Santos S, Zhang Y, Cao R, Hu P, Zheng J, Torres J, Kasabyan A, Lai LL, Yee LD, Wang LV. Panoramic photoacoustic computed tomography with learning-based classification enhances breast lesion characterization. Nat Biomed Eng. 2026 Jan;10(1):161-177. doi: 10.1038/s41551-025-01435-3. Epub 2025 Jun 24. PMID: 40555759.

Chen P, Chai J, Soundararajan A, Hepfer RG, Kheyfets B, Hu J, Alshanqiti I, Raman S, Tosa I, Huh JT, Yee M, Damon BJ, Wang S, Kim YS, Chung MK, Embree MC, Lee JS, Ye T, Yao H. Multiscale 3D Whole Joint Cellular and Molecular Mapping Reveals Disease-Specific Neurovascular Plasticity Underlying the Structure-Pain Relationship. Adv Sci (Weinh). 2026 Jan;13(1):e11226. doi: 10.1002/advs.202511226. Epub 2025 Nov 6. PMID: 41199410; PMCID: PMC12767019.

Chen P, Park S, Mert Cam R, Huang HK, Oraevsky AA, Villa U, Anastasio MA. Learning a Filtered Backprojection Reconstruction Method for Photoacoustic Computed Tomography With Hemispherical Measurement Geometries. IEEE Trans Med Imaging. 2026 Jan;45(1):70-82. doi: 10.1109/TMI.2025.3591706. PMID: 40694457; PMCID: PMC12947297.

Date unspecified

Cao H, Spitz S, Yu LY, Liu K, Zhang Z, Presutti F, Pramotton FM, Kulkarni S, Kamm RD, You S. Self-localized ultrafast pencil beam for volumetric multiphoton imaging. Nat Methods. 2026. [Epub ahead of print].

2025

December

Jia D, Dong D, Li T, Zong H, Zhu J, Teng X, Tian L, Cheng JX. Mid-infrared photothermal relaxation intensity diffraction tomography for video-rate volumetric chemical imaging. arXiv [Preprint]. 2025 Dec 30. Available from: https://arxiv.org/abs/2512.24375

Cam RM, Park S, Villa U, Anastasio MA. Application of a virtual imaging framework for investigating a deep learning-based reconstruction method for 3D quantitative photoacoustic computed tomography. Photoacoustics. 2025 Dec 29;48:100792. doi: 10.1016/j.pacs.2025.100792. PMID: 41626289; PMCID: PMC12858365.

Bower AJ, Zhang F, Liu T, Li J, Aguilera N, Abouassali S, Krynitsky J, Pursley R, Pohida T, Kowalski B, Lu R, Dubra A, Tam J. Surpassing the diffraction limit for improved lateral resolution in adaptive optics optical coherence tomography of the living human eye. Commun Eng. 2025 Dec 29;5(1):3. doi: 10.1038/s44172-025-00573-5. PMID: 41461899; PMCID: PMC12764984.

Boucau J, Ruelas Castillo J, Naidoo T, Liu Y, Dasgupta S, Jain N, Jacobson NE, Nargan K, Cimini BA, Eliceiri KW, Steyn AJC, Barczak AK. Inflammatory Macrophages Associate With Tissue Injury and Fibrosis in a Mouse Model of Tuberculosis. J Infect Dis. 2025 Dec 20;232(6):1375-1388. doi: 10.1093/infdis/jiaf361. PMID: 40629518; PMCID: PMC12718066.

Goswami N, Anastasio MA. LensPlus: a high space-bandwidth optical imaging technique. Biomed Opt Express. 2025 Dec 15;17(1):265-281. doi: 10.1364/BOE.580164. PMID: 41532106; PMCID: PMC12795420.

Ho RJ, Yeh K, Bhargava R. Time-Domain Quantum Cascade Laser-Based Vibrational Circular Dichroism Spectroscopy with Linear Dichroism Monitoring. Anal Chem. 2025 Dec 9;97(48):26748-26758. doi: 10.1021/acs.analchem.5c05477. Epub 2025 Nov 24. PMID: 41283682.

Umezu K, Brooks FJ, Larina I. In vivo volumetric visualization and quantification of cumulus expansion in mice with intravital optical coherence tomography. Biomed Opt Express. 2025 Dec 3;17(1):38-48. doi: 10.1364/BOE.580418. PMID: 41532112; PMCID: PMC12795421.

DeStefanis RA, Schmitz AE, Steimle AK, Payne SN, Sha GC, Olson AM, Cornelio A, Lippert AEL, Kraus SG, Johnson KA, Favreau PF, Gillette A, Babiarz C, Miller D, Sprackling CM, Pasch CA, Pritzl S, Van De Hey DR, Korkos DP, Foley TM, Yueh AE, Greane ALJX, Clipson L, Skala MC, Deming DA. BCL-2 Family Inhibition Enhances mTORC1/2 Inhibition in PIK3CA-Mutant Colorectal Cancer. Mol Cancer Ther. 2025 Dec 2;24(12):1914-1927. doi: 10.1158/1535-7163.MCT-24-1096. PMID: 40635161; PMCID: PMC12767208.

Guo Z, Chiesa G, Cheng JX. Feeling the vibes: vibrational spectroscopic imaging of biomolecular assemblies in their natural environment. Appl Phys Rev. 2025 Dec 1;12(4):041312. doi:10.1063/5.0244025

Aceto A, Wang Y, Yang D. An Integrative Drug-Induced Transcriptomic Analysis Identifies Novel MYC Antagonists and Potential Synergistic Drug Combinations. Mol Carcinog. 2025 Dec;64(12):2052-2062. doi: 10.1002/mc.70044. Epub 2025 Sep 30. PMID: 41025936; PMCID: PMC12639535.

Pham DL, Gillette AA, Riendeau J, Wiech K, Guzman EC, Datta R, Skala MC. Perspectives on label-free microscopy of heterogeneous and dynamic biological systems. J Biomed Opt. 2025 Dec;29(Suppl 2). doi: 10.1117/1.JBO.29.S2.S22702. Epub 2024 Feb 29. PMID: 38434231; PMCID: PMC10903072.

November

Eberman CC, Liu Y, Eliceiri KW, Witzenburg CM. Regional and temporal changes in early structural remodeling following myocardial infarction via semi-automatic image analysis.CardiovascPathol.2026Mar-Apr;81:107801.doi:10.1016/j.carpath.2025. 107801. Epub 2025 Nov 22. PMID: 41285368; PMCID: PMC12867677.

Wang X, Meng Y, Sun M, Gao X, Wang Y, Wang S, Wang K, Wang R, Ren D, Yin Y, Li C, Chen R, Wang LV, Shi J. Cross-regional real-time visualization of systemic physiology and dynamics with 3D panoramic photoacoustic computed tomography (3D-PanoPACT). Nat Commun. 2025 Nov 18;16(1):10077. doi: 10.1038/s41467-025-65054-x. PMID: 41253789; PMCID: PMC12627095.

Gillette A, Udgata S, Schmitz AE, Stoecker JN, Kratz JD, Deming DA, Skala MC. Wide-Field Optical Redox Imaging with Leading-Edge Detection Enables Assessment of Treatment Response and Heterogeneity in Patient-Derived Cancer Organoids. Cancer Res. 2025 Nov 14;85(22):4329-4340. doi: 10.1158/0008-5472.CAN-24-4958. PMID: 40920506; PMCID: PMC12478055.

Tang R, Yin J, Weinberg B, Lin H, Lu J, Gate D, Klementieva O, Cheng JX. Mid-Infrared Photothermal Mesoscopy with Millimeter Field of View and Sub-micron Spatial Resolution. bioRxiv [Preprint]. 2025 Nov 5:2025.11.03.686410. doi: 10.1101/2025.11.03.686410. PMID: 41279882; PMCID: PMC12637633.

Siddiqui AR, Roberts J, N'Diaye J, Ferris AL, Martin K, Putnam ST, Bhargava R, Dawlaty J, Zimmerman SC, Augustyn V, Rodríguez-López J. Real-time monitoring of the reversible capture and release of CO2 on anthraquinone and riboflavin-modified graphitic electrodes using ATR-SEIRAS. Chem Sci. 2025 Nov 4;16(48):23189-23202. doi: 10.1039/d5sc05427c. PMID: 41195072; PMCID: PMC12584010.

De la Cadena A, Park J, Shi J, Boppart SA. On the importance of simultaneous label-free multimodal nonlinear optical imaging for biomedical applications. APL Photonics. 2025 Nov 1;10(11):110902. doi: 10.1063/5.0289864. Epub 2025 Nov 18. PMID: 41282567; PMCID: PMC12632184.

Wei Y, Ahmed S, Rouco-Crenshaw S, Levin Y, Garibyan L, Sun C, et al. 234 Non-Invasive Biomarker Assessments Obtained Using Multiphoton Imaging in a Non-Interventional Clinical Study of Atopic Dermatitis. Journal of Investigative Dermatology. 2025 Nov 1;145(11):e68. doi:10.1016/j.jid.2025.09.238

Li J, Eliceiri K, Shribak M, Loeffler A, Wang Y. 51 Seeing Beyond H&E: Polychromatic PolScope Microscopy Visualizes Distinct Collagen Fiber Signatures in Colorectal Adenocarcinoma. American Journal of Clinical Pathology. 2025 Nov 1;164(Supplement_1):aqaf121.119. doi:10.1093/ajcp/aqaf121.119

Shao Z, Sengupta S, Anastasio MA, Li H. Semi-supervised semantic segmentation of cell nuclei with diffusion model and collaborative learning. J Med Imaging (Bellingham). 2025 Nov;12(6):061403. doi: 10.1117/1.JMI.12.6.061403. Epub 2025 Mar 20. PMID: 40124853; PMCID: PMC11924957.

Fayyaz M, Smith AM. Drug depots for obesity targeting metabolism, appetite, and inflammation. Expert Opin Drug Deliv. 2025 Nov;22(11):1617-1623. doi: 10.1080/17425247.2025.2554718. Epub 2025 Sep 6. PMID: 40874405; PMCID: PMC12781128.

Neubert JK, Allen K, Alliston T, Almarza AJ, Athanasiou KA, Donertas-Ayaz B, de Paula BB, Bavarian R, Bhutani N, Cairns BE, Caudle RM, Chai Y, Chen JF, Chen Y, Clark GT, Cruz-Almeida Y, DaSilva AF, Durham PL, Estela AV, Embree M, Fillingim R, Guastaldi F, Handa S, Kapila SD, Keith D, Kirkwood KL, Kramer P, Martucci KT, Murphy NP, Nackley AG, Ohrbach R, Sagl B, Smith SB, Tao F, Winkelstein B, Yao H, Young S, Gold MS. Preclinical perspectives on disorders of the temporomandibular joint: Tracing the past, navigating the present, and shaping the future. J Pain. 2025 Nov;36:105560. doi: 10.1016/j.jpain.2025.105560. Epub 2025 Sep 13. PMID: 40953762; PMCID: PMC12677152.

October

Haynes EM, Steinhauser C, Swader R, Petry G, Ulland TK, Eliceiri KW. Non-invasive longitudinal imaging reveals aging-associated changes in neuroimmune cells in adult zebrafish. bioRxiv [Preprint]. 2025 Oct 20:2025.09.23.676912. doi: 10.1101/2025.09.23.676912. PMID: 41040333; PMCID: PMC12485939.

Marcelino K, Sugimura M, Ocaya C, Sadat K, Romero R, Kim Y, Gnesda M, Konecny K, Kim K, Lietman TM, Rajadhyaksha M, Chidambaram JD, Kang D. Portable in vivo confocal ophthalmoscope for non-contact imaging of the cornea and anterior segment of the eye. Biomed Opt Express. 2025 Oct 15;16(11):4457-4469. doi: 10.1364/BOE.578730. PMID: 41293685; PMCID: PMC12643001.

Zhou M, Dong B, Lukov L, Ma S, He X, Zhang C. Interface-Sensitive Epi-Coherent Anti-Stokes Raman Scattering Microscopy for Imaging Cell Adhesion Dynamics. bioRxiv [Preprint]. 2025 Oct 14:2025.10.13.682172. doi: 10.1101/2025.10.13.682172. Update in: Anal Chem. 2026 Mar 17;98(10):7294-7303. doi: 10.1021/acs.analchem.5c06485. PMID: 41278803; PMCID: PMC12632835.

Huang HK, Kuo J, Park S, Villa U, Wang LV, Anastasio MA. Stochastic numerical head phantoms to enable virtual imaging studies of transcranial photoacoustic computed tomography. ArXiv [Preprint]. 2025 Oct 10:arXiv:2510.09758.

Pineda Guzman RA, Ostadi Moghaddam A, Confer MP, Majumdar S, Bhargava R, Wagoner Johnson AJ, Damon BM, Kersh ME. Non-invasive detection of local microstructural damage in tendon via Diffusion Tensor MRI. bioRxiv [Preprint]. 2025 Oct 10:2025.10.10.681653. doi:10.1101/2025.10.10.681653.

Polanco ER, Moustafa TE, Balcioglu O, Scherer SD, Cortes-Sanchez E, Remick S, Spike BT, Welm AL, Welm BE, Bernard PS, Zangle TA. Determination of Drug Sensitivity in Patient Derived Models of Breast Cancer by Multiparametric QPI. bioRxiv [Preprint]. 2025 Oct 1:2025.10.01.674349. doi: 10.1101/2025.10.01.674349. PMID: 41256452; PMCID: PMC12621830.

Sengupta S, Xu J, Nguyen P, Brooks F, Liu Y, Anastasio MA. On the utility of virtual staining for downstream applications as it relates to task network capacity. Biomed Opt Express. 2025 Oct 1;16(10):4224-4242. doi: 10.1364/BOE.576061. PMID: 41112785; PMCID: PMC12532334.

Edmonds H, Mukherjee SS, Holcombe B, Yeh K, Bhargava R, Ghosh A. Quantification of Protein Secondary Structures from Discrete Frequency Infrared Images Using Machine Learning. Appl Spectrosc. 2025 Oct;79(10):1465-1477. doi: 10.1177/00037028251325553. Epub 2025 Mar 31. PMID: 40165369; PMCID: PMC12353105.

Mitchell SJ, Pardo-Pastor C, Tchoumakova A, Zangle TA, Rosenblatt J. Energy deficiency selects crowded live epithelial cells for extrusion. Nature. 2025 Oct;646(8087):1187-1194. doi: 10.1038/s41586-025-09514-w. Epub 2025 Sep 10. PMID: 40931070; PMCID: PMC12571905.

Brasier N, Domenghino A, Meier CA, Jacob C, Xu S, Rogers JA. Implementing clinical needs into the development of wearable health-monitoring technology. Nat Nanotechnol. 2025 Oct;20(10):1350-1353. doi: 10.1038/s41565-025-02020-0. PMID: 41094259.

September

Xu P, Xi Y, Kim JW, Zhang M, Gao C, Wang Y, Xu M, Wang X, Ren S, Yang D, Wang Q, Xie W. A loss-of-function human ADAR variant activates innate immune response and promotes bowel inflammation. Nat Commun. 2025 Sep 29;16(1):8560. doi: 10.1038/s41467-025-63554-4. PMID: 41022715; PMCID: PMC12480066.

Applegate CC, Kang Y, Deng H, Chen D, Gonzalez Medina NY, Cui Y, Feng Y, Kuo CW, Shahoei SH, Kim H, Vidana Gamage HE, Wallig MA, Nelson ER, Swanson KS, Smith AM. Nanomedicine targeting PPAR in adipose tissue macrophages improves lipid metabolism and obesity-induced metabolic dysfunction. Sci Adv. 2025 Sep 26;11(39):eads3731. doi: 10.1126/sciadv.ads3731. Epub 2025 Sep 26. PMID: 41004576; PMCID: PMC12466850.

Hsieh PH, Hsieh SA, Richard C, Prasanth KV, Anderson JL, Bhargava R. Monitoring Molecular Uptake and Cancer Cells' Response by Development of Quantitative Drug Derivative Probes for Chemical Imaging. Anal Chem. 2025 Sep 23;97(37):20029-20038. doi: 10.1021/acs.analchem.5c00863. Epub 2025 Sep 9. PMID: 40923372; PMCID: PMC12788957.

Mohn KJ, Dong B, Mahapatra S, Singh IK, Lomont JP, Wan B, Zhang C. Spontaneous or Stimulated? Investigating Raman's Detection Limits in Aqueous Environments. J Phys Chem B. 2025 Sep 18;129(37):9446-9456. doi: 10.1021/acs.jpcb.5c04308. Epub 2025 Sep 3. PMID: 40899595; PMCID: PMC12781129.

Gomes C, Huang KC, Lavekar SS, Harkin J, Prosser CG, Fang Y, Kalem C, Oblak A, Zhang C, Meyer JS. Modeling human retinal ganglion cell axonal outgrowth, development, and pathology using pluripotent stem cell-based microfluidic platforms. Proc Natl Acad Sci U S A. 2025 Sep 16;122(37):e2423682122. doi: 10.1073/pnas.2423682122. Epub 2025 Sep 9. PMID: 40924455; PMCID: PMC12452894.

Pham DL, Cappabianca D, Forsberg MH, Weaver C, Mueller KP, Tommasi A, Vidugiriene J, Lauer A, Sylvester K, Lika J, Bugel M, Fan J, Capitini CM, Saha K, Skala MC. Label-free metabolic imaging monitors the fitness of chimeric antigen receptor T cells. Nat Biomed Eng. 2025 Sep 16:10.1038/s41551-025-01504-7. doi: 10.1038/s41551-025-01504-7. Epub ahead of print. PMID: 40958004; PMCID: PMC12445593.

Arogundade OH, Kuo CW, Cui Y, Sarkar S, Feng Y, Kolossov VL, James S, Lee W, Smith AM. Dynamic Polymer Cross-linking Limits the Homogeneity of Compact Quantum Dots for Single-Particle Tracking. ACS Appl Mater Interfaces. 2025 Sep 10;17(36):50476-50489. doi: 10.1021/acsami.5c12678. Epub 2025 Aug 29. PMID: 40878938; PMCID: PMC12781127.

Ledo AM, Misiewicz G, Dimke T, Tschantz WR, Handel J, Pelis R, Bruin G, Bechtold-Peters K, Sanchez-Felix M, Deshmukh S, Kim S, Proestaki M, Kamm RD. Utility of an in vitro lymphatics on-chip model for rank ordering subcutaneous absorption of monoclonal antibodies. Lab Chip. 2025 Sep 9;25(18):4660-4676. doi: 10.1039/d4lc00988f. PMID: 40755445; PMCID: PMC12771666.

Ghai A, Zheleznyak A, Egbulefu C, Blasi N, Black K, Tang R, Cooper ML, Vij K, Vij R, DiPersio J, Shokeen M, Achilefu S. Chemo-RaST with bortezomib inhibits multiple myeloma relapse. Theranostics. 2025 Sep 8;15(18):9911-9921. doi: 10.7150/thno.111508. PMID: 41041064; PMCID: PMC12486394.

Li C, Wang H, Song Z, Zhang W, Pan Y, Zhao Z, Qiu C, Yin K, Han M, Wang AB, Luan H, Li J, Yan W, Chen S, Shen H, Liu TL, Lee SSM, Ding W, Huang Y, Rogers JA, Wu C, Ni X. Wireless, wearable elastography via mechano-acoustic wave sensing for ambulatory monitoring of tissue stiffness. Sci Adv. 2025 Sep 5;11(36):eady0534. doi: 10.1126/sciadv.ady0534. Epub 2025 Sep 3. PMID: 40901956; PMCID: PMC12407073.

Min H, Wang Y, Wang J, Li X, Kim W, Aydin O, Kang S, You JS, Lim J, Wolhaupter K, Xu Y, Zhu Z, Gu J, Li X, Kim Y, Rao T, Kong HJ, Saif TA, Huang Y, Rogers JA, Bashir R. Optogenetic neuromuscular actuation of a miniature electronic biohybrid robot. Sci Robot. 2025 Sep 3;10(106):eadu5830. doi: 10.1126/scirobotics.adu5830. Epub 2025 Sep 3. PMID: 40901977; PMCID: PMC12767209.

Wang X, Wang Z, Li S, Pattarayan D, Wang Y, Zhai J, Zhang Y, Wang H, Xu M, Zhu J, Wang J, Ma X, Mani S, Xie W, Zhang M, Yang D. Publisher Correction: Cytoplasmic PXR regulates glucose metabolism by binding mRNAs and modulating their stability. Nat Struct Mol Biol. 2025 Sep;32(9):1840. doi: 10.1038/s41594-025-01668-5. Erratum for: Nat Struct Mol Biol. 2025 Nov;32(11):2144-2157. doi: 10.1038/s41594-025-01614-5. PMID: 40825880; PMCID: PMC12797102.

Min S, An J, Lee JH, Kim JH, Joe DJ, Eom SH, Yoo CD, Ahn HS, Hwang JY, Xu S, Rogers JA, Lee KJ. Publisher Correction: Wearable blood pressure sensors for cardiovascular monitoring and machine learning algorithms for blood pressure estimation. Nat Rev Cardiol. 2025 Sep;22(9):693. doi: 10.1038/s41569-025-01189-0. Erratum for: Nat Rev Cardiol. 2025 Sep;22(9):629-648. doi: 10.1038/s41569-025-01127-0. PMID: 40615731.

August

Tan KKD, De la Cadena A, Aksamitiene E, Ho A, Boppart SA. Simultaneous Label-Free Autofluorescence Multi-Harmonic Microscopy. J Vis Exp. 2025 Aug 29;(222):10.3791/68637. doi: 10.3791/68637. PMID: 40952928; PMCID: PMC12624867.

Zhang Y, Wang LV. Emerging Photoacoustic Imaging Techniques for Peripheral Arterial Disease. Curr Treat Options Cardiovasc Med. 2025;27(1):56. doi: 10.1007/s11936-025-01113-2. Epub 2025 Aug 28. PMID: 40893482; PMCID: PMC12394336.

Cui M, Kahraman SS, Wang LV. Optical focusing into scattering media via iterative time reversal guided by absorption nonlinearity. Nat Commun. 2025 Aug 21;16(1):7807. doi: 10.1038/s41467-025-63095-w. PMID: 40841371; PMCID: PMC12370915.

Wu M, Zhang K, Fok PJY, Zhang H, Efimov AI, Wang Y, Feng J, Li S, Gu J, Lu X, Hintermueller D, Zeng L, Zhang J, Waters EA, Yang T, Liu J, Wang G, Lv Z, Wei Y, Yang Y, Haney CR, Kozorovitskiy Y, Avila R, Vázquez-Guardado A, Huang Y, Rogers JA. Analysis and management of thermal loads generated in vivo by miniaturized optoelectronic implantable devices. Device. 2025 Aug 21:100898. doi: 10.1016/j.device.2025.100898. Epub ahead of print. PMID: 40881673; PMCID: PMC12376052.

Zhang H, Zhang K, Wu M, Li S, Bodkin KL, Kozorovitskiy Y, Rogers JA, Huang Y. Analytical solutions for light propagation of LED. Proc Natl Acad Sci U S A. 2025 Aug 19;122(33):e2508163122. doi: 10.1073/pnas.2508163122. Epub 2025 Aug 13. PMID: 40802683; PMCID: PMC12377766.

Nelson RS, Grossman MG, Klug ZM, Calamari M, Donayre A, Cybulski T, Schooley J, Griffith GJ, Corcos DM, Wright DE, Wallace JC, Yang DS, Wright JA Jr, Rogers JA, Lee SP, Ghaffari R, Aranyosi AJ, Jain M. Remote analysis and management of sweat biomarkers using a wearable microfluidic sticker in adult cystic fibrosis patients. Proc Natl Acad Sci U S A. 2025 Aug 19;122(33):e2506137122. doi: 10.1073/pnas.2506137122. Epub 2025 Aug 12. PMID: 40794828; PMCID: PMC12377746.

Gensemer C, Petrucci T, Beck T, Daylor V, Griggs M, Griggs C, Weintraub A, Byerly K, Guo L, Morningstar J, Kornblau I, Biggs R, Moore K, Koren N, Hastings C, Oberlies E, Zientara ER, Devey E, Dooley S, Stayer K, Fenner R, Singleton K, Luzbetak S, Bear D, Byrd R, Weninger J, Bistran E, Beeson G, Kerns J, Osterhaus M, Fleck E, Schnaudigel J, Butler S, Severance S, Kendall W, Delaney JR, Judge DP, Chen P, Yao H, Guz J, Awgulewitsch A, Kautz SA, Mukherjee R, Price R, Henderson F Sr, Shapiro S, Francomano CA, Kovacic JC, Lavallee M, Kontorovich AR, Berrandou TE, Slaugenhaupt SA, Milan D, Maitland A, Patel S, Bouatia-Naji N, Norris RA. KLK15 alters connective tissues in hypermobile Ehlers-Danlos syndrome. iScience. 2025 Aug 12;28(9):113343. doi: 10.1016/j.isci.2025.113343. PMID: 40949095; PMCID: PMC12424230.

Pattarayan D, Wang Y, Wang Z, Li S, Wang X, Chen Y, Wang Y, Chen CY, Bhuniya A, Yadav GS, Xie W, Kammula US, Li S, Zhang M, Yang D. The lncRNA EPIC1 suppresses dsRNA-induced type I IFN signaling and is a therapeutic target to enhance TNBC response to PD-1 inhibition. Sci Signal. 2025 Aug 12;18(899):eadr9131. doi: 10.1126/scisignal.adr9131. Epub 2025 Aug 12. PMID: 40794843; PMCID: PMC12640557

Datta R, Miskolci V, Gallego-López GM, Britt E, Gillette A, Kralovec A, Giese MA, Qian T, Votava J, Zhao W, Fan J, Huttenlocher A, Skala MC. Single cell autofluorescence imaging reveals immediate metabolic shifts of neutrophils with activation across biological systems. Front Immunol. 2025 Aug 7;16:1617993. doi: 10.3389/fimmu.2025.1617993. PMID: 40852713; PMCID: PMC12367685.

Sutton CM, Umezu K, Mashiko D, Ikawa M, Larina IV, Garcia TX, Matzuk MM. Rescue of male infertility by human PRSS55 in transgenic mice establishes a contraceptive research model. Sci Rep. 2025 Aug 5;15(1):28657. doi: 10.1038/s41598-025-09604-9. PMID: 40764777; PMCID: PMC12325665.

Kim M, López-Cano M, Zhang K, Wang Y, Gómez-Santacana X, Flores Á, Wu M, Li S, Zhang H, Wei Y, Li X, Good CH, Banks AR, Llebaria A, Hernando J, Sunwoo SH, Gu J, Huang Y, Ciruela F, Rogers JA. Wireless, battery-free, remote photoactivation of caged-morphine for photopharmacological pain modulation without side effects. Biosens Bioelectron. 2025 Aug 1;281:117440. doi: 10.1016/j.bios.2025.117440. Epub 2025 Apr 4. PMID: 40220492; PMCID: PMC12767206.

Chitsaz M, Yang L, Rayes-Danan R, Savari O, Li B, Shribak M, Eliceiri K, Loeffler A. Polychromatic Polarization Microscopy Differentiates Collagen Fiber Signatures in Benign Pancreatic Tissue and Pancreatic Ductal Adenocarcinoma. Mod Pathol. 2025 Aug;38(8):100768. doi: 10.1016/j.modpat.2025.100768. Epub 2025 Apr 8. PMID: 40210130; PMCID: PMC12767205.

Zwi-Dantsis L, Jayarajan V, Church GM, Kamm RD, de Magalhães JP, Moeendarbary E. Aging on Chip: Harnessing the Potential of Microfluidic Technologies in Aging and Rejuvenation Research. Adv Healthc Mater. 2025 Aug;14(20):e2500217. doi: 10.1002/adhm.202500217. Epub 2025 Jun 12. PMID: 40509615; PMCID: PMC12333483.

July

Li S, Wang Z, Wang X, Wang Y, Pattarayan D, Zhang Y, Nguyen P, Bhuniya A, Chen Y, Huang H, Huang Y, Wang L, Wang J, Li S, Zhang M, Liu Y, Lee N, Yang D. Integrative characterization of MYC RNA-binding function. Cell Genom. 2025 Jul 9;5(7):100878. doi: 10.1016/j.xgen.2025.100878. Epub 2025 May 15. PMID: 40378850; PMCID: PMC12278643.

Sivaguru M, Schrup SE, Fouke KW, Sherman ME, Samuel AZ, Maimone S, Bhargava R, Fouke BW. Mechanisms of osteopontin-stabilized amorphous calcium phosphate calcification in benign and pre-malignant breast disease. Sci Rep. 2025 Jul 4;15(1):23849. doi: 10.1038/s41598-025-08903-5. PMID: 40615470; PMCID: PMC12227591.

Kumar A, Mondal S, Khatua D, Guha D, Mukherjee B, Lahiri A, Prasad DK, Sekh AA. AI-driven analysis by identifying risk factors of VL relapse in HIV co-infected patients. Sci Rep. 2025 Jul 1;15(1):21067. doi: 10.1038/s41598-025-07406-7. PMID: 40596278; PMCID: PMC12215746.

Qian G, Zhang H, Liu Y, Shribak M, Eliceiri KW, Provenzano PP. Computationally Enabled Polychromatic Polarized Imaging Enables Mapping of Matrix Architectures that Promote Pancreatic Ductal Adenocarcinoma Dissemination. Am J Pathol. 2025 Jul;195(7):1242-1253. doi: 10.1016/j.ajpath.2025.04.017. Epub 2025 May 9. PMID: 40350060; PMCID: PMC12264559.

June

Feng Y, Chen D, Applegate C, Gonzalez Medina N, Kuo CW, Arogundade OH, Wright CL, Xu F, Drnevich J, Smith AM. Nanocoding: Lipid Nanoparticle Barcoding for Multiplexed Single-Cell RNA Sequencing. ACS Nano. 2025 Jun 24;19(24):22079-22092. doi: 10.1021/acsnano.5c02111. Epub 2025 Jun 9. PMID: 40489257; PMCID: PMC12767207.

Yang L, Sorrells JE, Iyer RR, Boppart SA. Polarimetric coherent anti-Stokes Raman scattering microscopy of collagen. Opt Lett. 2025 Jun 15;50(12):4010-4013. doi: 10.1364/OL.557999. PMID: 40512930; PMCID: PMC12767204.

Nichols JH, Smith AM, Jonsson CB. The Intersection of SARS-CoV-2 and Diabetes. Microorganisms. 2025 Jun 14;13(6):1390. doi: 10.3390/microorganisms13061390. PMID: 40572277; PMCID: PMC12196163.

Gokhale Y, Coventry BS, Rogers T, Lines M, Vena A, Phillips J, Zhu T, Bok I, Troche D, Glodowski M, Vareberg A, Bhatt S, Ashtiani AO, Eliceiri KW, Hai A. Self-Aligned Multilayered Nitrogen Vacancy Diamond Nanoparticles for High Spatial Resolution Magnetometry of Microelectronic Currents. Nano Lett. 2025 Jun 11;25(23):9204-9213. doi: 10.1021/acs.nanolett.5c00656. Epub 2025 May 19. PMID: 40387807; PMCID: PMC12164517.

Chen M, Ma H, Sun X, Schwartz M, Brand RE, Xu J, Gotsis DS, Nguyen P, Moore BA, Snyder L, Brand RM, Liu Y. Multimodal whole slide image processing pipeline for quantitative mapping of tissue architecture and tissue microenvironment. Npj Imaging. 2025 Jun 10;3:26. doi: 10.1038/s44303-025-00088-w. PMID: 40510252; PMCID: PMC12151862.

Galdino FE, Rabelo RS, Scarpa I, Yoneda JS, Consonni SR, Paes Leme AF, Smith AM, Harkiolaki M, Cardoso MB. Internalization and Cellular Fate of Protein Corona-Coated Nanoparticles by Multimodal Multi-Scale Microscopy. Small. 2025 Jun;21(22):e2409065. doi: 10.1002/smll.202409065. Epub 2024 Dec 8. PMID: 39648571; PMCID: PMC12140912.

May

Aksamitiene E, Park J, Marjanovic M, Boppart SA. Defining Biological Variability, Analytical Precision and Quantitative Biophysiochemical Characterization of Human Urinary Extracellular Vesicles. J Extracell Vesicles. 2025 May;14(5):e70087. doi: 10.1002/jev2.70087. PMID: 40384173; PMCID: PMC12086329.

April

Lika J, Votava JA, Datta R, Mellado Fritz CA, Kralovec AM, Smith FM, Huttenlocher A, Skala MC, Fan J. Mitochondrial metabolism is rapidly re-activated in mature neutrophils to support stimulation-induced response. Front Immunol. 2025 Apr 28;16:1572927. doi: 10.3389/fimmu.2025.1572927. PMID: 40356902; PMCID: PMC12066771.

Scully DM, Xia T, Musina GR, McCown MA, Umezu K, Kircher BK, Behringer RR, Larina IV. Region-specific roles of oviductal motile cilia in oocyte/embryo transport and fertility†. Biol Reprod. 2025 Apr 13;112(4):651-662. doi: 10.1093/biolre/ioaf005. PMID: 39761349; PMCID: PMC11996758.

Kratz JD, Rehman S, Johnson KA, Gillette AA, Sunil A, Favreau PF, Pasch CA, Miller D, Zarling LC, Yeung AH, Clipson L, Anderson SJ, Steimle AK, Sprackling CM, Lemmon KK, Abbott DE, Burkard ME, Bassetti MF, Eickhoff JC, Foley EF, Heise CP, Kimple RJ, Lawson EH, LoConte NK, Lubner SJ, Mulkerin DL, Matkowskyj KA, Sanger CB, Uboha NV, Mcilwain SJ, Ong IM, Carchman EH, Skala MC, Deming DA. Subclonal response heterogeneity to define cancer organoid therapeutic sensitivity. Sci Rep. 2025 Apr 9;15(1):12072. doi: 10.1038/s41598-025-96204-2. PMID: 40200028; PMCID: PMC11978853.

Schmitz RL, Riendeau JM, Tweed KE, Rehani P, Samimi K, Pham DL, Jones I, Maly EM, Contreras Guzman E, Forsberg MH, Shahi A, Hockerman L, Ayuso JM, Capitini CM, Walsh AJ, Skala MC. Autofluorescence lifetime imaging classifies human B and NK cell activation state. Front Bioeng Biotechnol. 2025 Apr 4;13:1557021. doi: 10.3389/fbioe.2025.1557021. PMID: 40256783; PMCID: PMC12006760.

Qian T, Desa DE, Guzman EC, Zhao W, Zhang X, Palecek SP, Skala MC. Label-free method to monitor metabolism during long-term culture of human pluripotent stem cell derived cardiomyocytes. Biophotonics Discov. 2025 Apr;2(2):025001. doi: 10.1117/1.bios.2.2.025001. Epub 2025 Apr 17. PMID: 40612252; PMCID: PMC12225635.

March

Renteria CA, Kahng J, Tibble B, Iyer RR, Shi J, Algrain H, Chaney EJ, Aksamitiene E, Liu YZ, Robinson P, Schmidt T, Boppart SA. Two-photon activation, deactivation, and coherent control of melanopsin in live cells. bioRxiv [Preprint]. 2025 Mar 30:2025.03.26.645437. doi: 10.1101/2025.03.26.645437. PMID: 40196647; PMCID: PMC11974792.

Brooks FJ, Deshpande R. Evaluation of Machine-generated Biomedical Imaging via A Tally-based Similarity Measure. ArXiv [Preprint]. 2025 Mar 28:arXiv:2503.22658v1. doi: 10.48550/arXiv.2503.22658.

Ayyadurai VAS, Deonikar P, Kamm RD. A molecular systems architecture of neuromuscular junction in amyotrophic lateral sclerosis. NPJ Syst Biol Appl. 2025 Mar 17;11(1):27. doi: 10.1038/s41540-025-00501-5. PMID: 40097438; PMCID: PMC11914587.

Mondal S, Khatua D, Mandal S, Prasad DK, Sekh AA. BMWP: the first Bengali math word problems dataset for operation prediction and solving. Discov Artif Intell. 2025;5(1):25. doi: 10.1007/s44163-025-00243-7. Epub 2025 Mar 13. PMID: 40092969; PMCID: PMC11903620.

Jeong G, Villa U, Anastasio MA. Revisiting the joint estimation of initial pressure and speed-of-sound distributions in photoacoustic computed tomography with consideration of canonical object constraints. Photoacoustics. 2025 Mar 6;43:100700. doi: 10.1016/j.pacs.2025.100700. PMID: 40454201; PMCID: PMC12126746.

De la Cadena A, Renteria CA, Aksamitiene E, Boppart SA. Label-free hyperspectral multiphoton microscopy. Opt Lett. 2025 Mar 1;50(5):1484-1487. doi: 10.1364/OL.547032. PMID: 40019961; PMCID: PMC12118598.

Kim J, Tian Y, Qiao G, Villarta JA, Zhao F, He A, Ho RJ, Liu H, Bhargava R, Zhang Y. Endoscopic Fourier-transform infrared spectroscopy through a fiber microprobe. Rev Sci Instrum. 2025 Mar 1;96(3):033702. doi: 10.1063/5.0233920. PMID: 40029128; PMCID: PMC13074160.

February

Souder DC, McGregor ER, Clark JP, Rhoads TW, Porter TJ, Eliceiri KW, Moore DL, Puglielli L, Anderson RM. Neuron-specific isoform of PGC-1α regulates neuronal metabolism and brain aging. Nat Commun. 2025 Feb 28;16(1):2053. doi: 10.1038/s41467-025-57363-y. PMID: 40021651; PMCID: PMC11871081.

Kang D, Da Silva A, Lynch J, Mallidi S, Pircher M, Saknite I. Introduction to the Biophotonics Congress 2024 feature issue. Biomed Opt Express. 2025 Feb 24;16(3):1158-1159. doi: 10.1364/BOE.559672. PMID: 40109523; PMCID: PMC11919367.

Huang HK, Kuo J, Zhang Y, Aborahama Y, Cui M, Sastry K, Park S, Villa U, Wang LV, Anastasio MA. Fast aberration correction in 3D transcranial photoacoustic computed tomography via a learning-based image reconstruction method. Photoacoustics. 2025 Feb 20;43:100698. doi: 10.1016/j.pacs.2025.100698. PMID: 40115737; PMCID: PMC11923815.

Riendeau JM, Gillette AA, Guzman EC, Cruz MC, Kralovec A, Udgata S, Schmitz A, Deming DA, Cimini BA, Skala MC. Cellpose as a reliable method for single-cell segmentation of autofluorescence microscopy images. Sci Rep. 2025 Feb 14;15(1):5548. doi: 10.1038/s41598-024-82639-6. PMID: 39952935; PMCID: PMC11828867.

Ramakrishnan G, Miskolci V, Hunter M, Giese MA, Münch D, Hou Y, Eliceiri KW, Lasarev MR, White RM, Huttenlocher A. J Cell Biol. 2025 Feb 3;224(2):e202403096. doi: 10.1083/jcb.202403096. Epub 2024 Nov 21. PMID: 39570286; PMCID: PMC11586626.

Shi J, Ho A, Snyder CE, Chaney EJ, Sorrells JE, Alex A, Talaban R, Spillman DR Jr, Marjanovic M, Doan M, Finka G, Hood SR, Boppart SA. Accelerating biopharmaceutical cell line selection with label-free multimodal nonlinear optical microscopy and machine learning. Commun Biol. 2025 Feb 3;8(1):157. doi: 10.1038/s42003-025-07596-w. PMID: 39900674; PMCID: PMC11790971.

Wagner AS, Smith FM, Bennin DA, Votava JA, Datta R, Giese MA, Zhao W, Skala MC, Fan J, Keller NP, Huttenlocher A. GATA1-deficient human pluripotent stem cells generate neutrophils with improved antifungal immunity that is mediated by the integrin CD18. PLoS Pathog. 2025 Feb 3;21(2):e1012654. doi: 10.1371/journal.ppat.1012654. PMID: 39899622; PMCID: PMC11825098.

Ma H, Nguyen P, Liu Y. A Versatile Drift-Free Super-Resolution Imaging Method via Oblique Bright-Field Correlation. Adv Sci (Weinh). 2025 Feb;12(7):e2412127. doi: 10.1002/advs.202412127. Epub 2024 Dec 24. PMID: 39716987; PMCID: PMC11831467.

Luo Y, Huang HK, Sastry K, Hu P, Tong X, Kuo J, Aborahama Y, Na S, Villa U, Anastasio MA, Wang LV. Full-Wave Image Reconstruction in Transcranial Photoacoustic Computed Tomography Using a Finite Element Method. IEEE Trans Med Imaging. 2025 Feb;44(2):645-655. doi: 10.1109/TMI.2024.3456595. Epub 2025 Feb 4. PMID: 39250376; PMCID: PMC11875890.

January

Lin H, Seitz S, Tan Y, Lugagne JB, Wang L, Ding G, He H, Rauwolf TJ, Dunlop MJ, Connor JH, Porco JA Jr, Tian L, Cheng JX. Nat Methods. 2025 Jan 16. doi: 10.1038/s41592-024-02575-1. Epub ahead of print. PMID: 39820753.

Huang H, Fang L, Wansapura J, Prior JL, Manion B, Xu B, Hongsermeier C, Gamadia N, Blasi N, Tang R, Egbulefu C, Shokeen M, Quirk JD, Achilefu S. Theranostics. 2025 Jan 1;15(4):1205-1220. doi: 10.7150/thno.99863. PMID: 39816680; PMCID: PMC11729564.

Makeev A, Li K, Anastasio MA, Emig A, Jahnke P, Glick SJ. J Med Imaging (Bellingham). 2025 Jan;12(Suppl 1):S13005. doi: 10.1117/1.JMI.12.S1.S13005. Epub 2024 Oct 15. PMID: 39416764; PMCID: PMC11474246.

Deshpande R, Kelkar VA, Gotsis D, Kc P, Zeng R, Myers KJ, Brooks FJ, Anastasio MA. Med Phys. 2025 Jan;52(1):4-20. doi: 10.1002/mp.17473. Epub 2024 Oct 24. PMID: 39447007; PMCID: PMC11699998.

Lange D, Judson-Torres R, Zangle TA, Lex A. Aardvark: Composite Visualizations of Trees, Time-Series, and Images. IEEE Trans Vis Comput Graph. 2025 Jan;31(1):1290-1300. doi: 10.1109/TVCG.2024.3456193. Epub 2024 Nov 25. PMID: 39255114; PMCID: PMC12143745.

Date unspecified

Wu T, Thornburg ZR, Tan K, Kenkel S, Boppart SA, Bhargava R, Luthey-Schulten Z. Visualizing cell structures with Minecraft. The Biophysicist, 6(1), 2025.

Falahkheirkhah K, Oh J, Bhargava R. Advancing trustworthy virtual staining in histopathology using infrared spectroscopic imaging. In: Spectroscopic Techniques for Cancer Diagnostics. Bristol (UK): IOP Publishing; 2025. p. 4-1-4-19. doi:10.1088/978-0-7503-5949-8ch4.

2024

December

Jia D, Cheng R, McNeely JH, Zong H, Teng X, Xu X, Cheng JX. Sci Adv. 2024 Dec 20;10(51):eadn8255. doi: 10.1126/sciadv.adn8255. Epub 2024 Dec 20. PMID: 39705354; PMCID: PMC11661430.

Liu K, Cao H, Shashaty K, Yu LY, Spitz S, Pramotton FM, Wan Z, Kan EL, Tevonian EN, Levy M, Lendaro E, Kamm RD, Griffith LG, Wang F, Qiu T, You S. Sci Adv. 2024 Dec 13;10(50):eadp2438. doi: 10.1126/sciadv.adp2438. Epub 2024 Dec 11. PMID: 39661679; PMCID: PMC11633739.

Cheng JX, Warren WS. Sci Adv. 2024 Dec 13;10(50):eadu9069. doi: 10.1126/sciadv.adu9069. Epub 2024 Dec 11. PMID: 39661680; PMCID: PMC11633730.

Scope Crafts E, Anastasio MA, Villa U. Inverse Probl. 2024 Dec 1;40(12):125012. doi: 10.1088/1361-6420/ad910a. Epub 2024 Nov 20. PMID: 39574468; PMCID: PMC11577155.

Weisbart E, Tromans-Coia C, Diaz-Rohrer B, Stirling DR, Garcia-Fossa F, Senft RA, Hiner MC, de Jesus MB, Eliceiri KW, Cimini BA. J Microsc. 2024 Dec;296(3):227-234. doi: 10.1111/jmi.13223. Epub 2023 Sep 23. PMID: 37690102; PMCID: PMC10924770.

Sivagurunathan S, Marcotti S, Nelson CJ, Jones ML, Barry DJ, Slater TJA, Eliceiri KW, Cimini BA. J Microsc. 2024 Dec;296(3):199-213. doi: 10.1111/jmi.13229. Epub 2023 Oct 12. PMID: 37727897; PMCID: PMC10950841.

Brasier N, Wang J, Gao W, Sempionatto JR, Dincer C, Ates HC, Güder F, Olenik S, Schauwecker I, Schaffarczyk D, Vayena E, Ritz N, Weisser M, Mtenga S, Ghaffari R, Rogers JA, Goldhahn J. Nature. 2024 Dec;636(8041):57-68. doi: 10.1038/s41586-024-08249-4. Epub 2024 Dec 4. PMID: 39633192.

November

Liu W, Ayupova T, Wang W, Shepherd S, Wang X, Akin LD, Kohli M, Demirci U, Cunningham BT. Dynamic and large field of view photonic resonator absorption microscopy for ultrasensitive digital resolution detection of nucleic acid and protein biomarkers. Biosens Bioelectron. 2024 Nov 15;264:116643. doi: 10.1016/j.bios.2024.116643. Epub 2024 Aug 8. PMID: 39146773.

Dickey AK, Berkovich J, Leaf RK, Jiang PY, Lopez-Galmiche G, Rebeiz L, Wheeden K, Kochevar I, Savage W, Zhao S, Campisi E, Heo SY, Trueb J, LaRochelle EPM, Rogers J, Banks A, Chang JK. Int J Dermatol. 2024 Nov;63(11):1584-1591. doi: 10.1111/ijd.17166. Epub 2024 Apr 11. PMID: 38602089; PMCID: PMC11467130.

October

Cheng JX, Chen TY, Chen P. The Evolution of Sub-diffraction Chemical Imaging from Nanoscale to AI. Chem Biomed Imaging. 2024 Oct 29;2(11):731-732. doi: 10.1021/cbmi.4c00079. PMID: 39610467; PMCID: PMC11600144.

Ma H, Chen M, Xu J, Yang Y, Zhao Y, Liu Y. Sci Adv. 2024 Oct 18;10(42):eadq5009. doi: 10.1126/sciadv.adq5009. Epub 2024 Oct 16. PMID: 39413179; PMCID: PMC11482309

Shmuylovich L, O'Brien CM, Nwosu K, Achilefu S. Sci Rep. 2024 Oct 17;14(1):24402. doi: 10.1038/s41598-024-75646-0. PMID: 39420102; PMCID: PMC11487067.

Mukherjee SS, Maleszewski JJ, Luthringer D, Confer MP, Mittal A, Dasari S, McPhail ED, Kapa S, Kesavadas T, Kajdacsy-Balla A, Kransdorf E, Raman J, Bhargava R. Circulation. 2024 Oct 15;150(16):1299-1301. doi: 10.1161/CIRCULATIONAHA.124.069554. Epub 2024 Oct 14. PMID: 39401277; PMCID: PMC11486296.

Cimini BA, Bankhead P, D'Antuono R, Fazeli E, Fernandez-Rodriguez J, Fuster-Barceló C, Haase R, Jambor HK, Jones ML, Jug F, Klemm AH, Kreshuk A, Marcotti S, Martins GG, McArdle S, Miura K, Muñoz-Barrutia A, Murphy LC, Nelson MS, Nørrelykke SF, Paul-Gilloteaux P, Pengo T, Pylvänäinen JW, Pytowski L, Ravera A, Reinke A, Rekik Y, Strambio-De-Castillia C, Thédié D, Uhlmann V, Umney O, Wiggins L, Eliceiri KW. J Cell Sci. 2024 Oct 15;137(20):jcs262322. doi: 10.1242/jcs.262322. Epub 2024 Oct 30. PMID: 39475207; PMCID: PMC11698046.

Erickson-Bhatt S, Cox BL, Macdonald E, Chacko JV, Begovatz P, Keely PJ, Ponik SM, Eliceiri KW, Fain SB. Metabolites. 2024 Oct 15;14(10):550. doi: 10.3390/metabo14100550. PMID: 39452931; PMCID: PMC11509230.

Ye M, Yang C, Cheng JX, Lee HJ, Jiang Y, Shi L. Front Cell Neurosci. 2024 Oct 3;18:1494457. doi: 10.3389/fncel.2024.1494457. PMID: 39421603; PMCID: PMC11484022.

Zaki FR, Monroy GL, Shi J, Sudhir K, Boppart SA. Texture-based speciation of otitis media-related bacterial biofilms from optical coherence tomography images using supervised classification. J Biophotonics. 2024 Oct;17(10):e202400075. doi: 10.1002/jbio.202400075. Epub 2024 Aug 5. PMID: 39103198; PMCID: PMC11464188.

Deshpande R, Ozbey M, Li H, Anastasio MA, Brooks FJ. IEEE Trans Med Imaging. 2024 Oct;43(10):3608-3620. doi: 10.1109/TMI.2024.3414931. Epub 2024 Oct 28. PMID: 38875086; PMCID: PMC11608762.

Wang G, Iyer RR, Sorrells JE, Aksamitiene E, Chaney EJ, Renteria CA, Park J, Shi J, Sun Y, Boppart SA, Tu H. Pixelation with concentration-encoded effective photons for quantitative molecular optical sectioning microscopy. Laser Photon Rev. 2024 Oct;18(10):2400031. doi: 10.1002/lpor.202400031. Epub 2024 Jul 3. PMID: 39781104; PMCID: PMC11706540.

September

Selzer GJ, Rueden CT, Hiner MC, Evans EL, Kolb D, Wiedenmann M, Birkhold C, Buchholz TO, Helfrich S, Northan B, Walter A, Schindelin J, Pietzsch T, Saalfeld S, Berthold MR, Eliceiri KW. Front Bioinform. 2024 Sep 27;4:1435733. doi: 10.3389/fbinf.2024.1435733. PMID: 39399098; PMCID: PMC11466933.

Das Gupta A, Park J, Sorrells JE, Kim H, Krawczynska N, Pradeep D, Wang Y, Vidana Gamage HE, Nelczyk AT, Boppart SA, Boppart MD, Nelson ER. Endocrinology. 2024 Sep 26;165(11):bqae127. doi: 10.1210/endocr/bqae127. PMID: 39298675; PMCID: PMC11448339.

Majer J, Alex A, Shi J, Chaney EJ, Mukherjee P, Spillman DR Jr, Marjanovic M, Newman CF, Groseclose RM, Watson PD, Boppart SA, Hood SR. Lab Chip. 2024 Sep 24;24(19):4594-4608. doi: 10.1039/d4lc00504j. PMID: 39258913.

Jeong G, Li F, Mitcham TM, Villa U, Duric N, Anastasio MA. IEEE Trans Ultrason Ferroelectr Freq Control. 2024 Sep 12;PP. doi: 10.1109/TUFFC.2024.3459391. Epub ahead of print. PMID: 39264782.

Avachat AV, Mahmoud KH, Leja AG, Xu JJ, Anastasio MA, Sivaguru M, Di Fulvio A. Sci Rep. 2024 Sep 10;14(1):21155. doi: 10.1038/s41598-024-71695-7. PMID: 39256482; PMCID: PMC11387643.

Khemtonglang K, Liu W, Lee H, Wang W, Li S, Li ZY, Shepherd S, Yang Y, Diel DG, Fang Y, Cunningham BT. Biomed Opt Express. 2024 Sep 5;15(10):5691-5705. doi: 10.1364/BOE.531388. PMID: 39421766; PMCID: PMC11482178.

Kadama-Makanga P, Semeere A, Laker-Oketta M, Mubiru M, Lukande R, Huchko M, Freeman E, Kulkarni N, Martin J, Kang D, Nakalembe M. BMC Womens Health. 2024 Sep 2;24(1):483. doi: 10.1186/s12905-024-03323-5. PMID: 39223605; PMCID: PMC11367841.

Adi W, Rubio Perez BE, Liu Y, Runkle S, Eliceiri KW, Yesilkoy F. J Biomed Opt. 2024 Sep;29(9):093511. doi: 10.1117/1.JBO.29.9.093511. Epub 2024 Sep 27. PMID: 39364328; PMCID: PMC11448345.

Li K, Li H, Anastasio MA. Investigating the use of signal detection information in supervised le Fast aberration correction in 3D transcranial photoacoustic computed tomography via a learning-based image reconstruction method arning-based image denoising with consideration of task-shift. J Med Imaging (Bellingham). 2024 Sep;11(5):055501. doi: 10.1117/1.JMI.11.5.055501. Epub 2024 Sep 5. PMID: 39247217; PMCID: PMC11376226.

Roh TT, Alex A, Chandramouleeswaran PM, Sorrells JE, Ho A, Iyer RR, Spillman DR Jr, Marjanovic M, Ekert JE, Sridharan B, Prabhakarpandian B, Hood SR, Boppart SA. Predicting DNA damage response in non-small cell lung cancer organoids via simultaneous label-free autofluorescence multiharmonic microscopy. Redox Biol. 2024 Sep;75:103280. doi: 10.1016/j.redox.2024.103280. Epub 2024 Jul 22. PMID: 39083897; PMCID: PMC11340607.

August

Mancha S, Horan M, Pasachhe O, Keikhosravi A, Eliceiri KW, Matkowskyj KA, Notbohm J, Skala MC, Campagnola PJ. Acta Biomater. 2024 Aug 23:S1742-7061(24)00470-7. doi: 10.1016/j.actbio.2024.08.026. Epub ahead of print. PMID: 39182805.

Gallego-López GM, Contreras Guzman E, Desa DE, Knoll LJ, Skala MC. Metabolic changes in Toxoplasma gondii-infected host cells measured by autofluorescence imaging. mBio. 2024 Aug 14;15(8):e0072724. doi: 10.1128/mbio.00727-24. Epub 2024 Jul 8. PMID: 38975793; PMCID: PMC11323734.

Renteria CA, Park J, Zhang C, Sorrells JE, Iyer RR, Tehrani KF, De la Cadena A, Boppart SA. Large field-of-view metabolic profiling of murine brain tissue following morphine incubation using label-free multiphoton microscopy. J Neurosci Methods. 2024 Aug;408:110171. doi: 10.1016/j.jneumeth.2024.110171. Epub 2024 May 21. PMID: 38777156; PMCID: PMC12047187.

Samimi K, Pasachhe O, Guzman EC, Riendeau J, Gillette AA, Pham DL, Wiech KJ, Moore DL, Skala MC. Cytometry A. 2024 Aug;105(8):607-620. doi: 10.1002/cyto.a.24883. Epub 2024 Jun 28. PMID: 38943226.

Pramotton FM, Spitz S, Kamm RD. Challenges and Future Perspectives in Modeling Neurodegenerative Diseases Using Organ-on-a-Chip Technology. Adv Sci (Weinh). 2024 Aug;11(32):e2403892. doi: 10.1002/advs.202403892. Epub 2024 Jun 23. PMID: 38922799; PMCID: PMC11348103.

Joshi H, Singh BP, Butola A, Surya V, Mishra D, Agarwal K, Mehta DS. J Biophotonics. 2024 Aug;17(8):e202400088. doi: 10.1002/jbio.202400088. Epub 2024 Jun 20. PMID: 38899690.

July

Iyer RR, Yang L, Sorrells JE, Chaney EJ, Spillman DR Jr, Boppart SA. Dispersion mismatch correction for evident chromatic anomaly in low coherence interferometry. APL Photonics. 2024 Jul 1;9(7):076114. doi: 10.1063/5.0207414. Epub 2024 Jul 23. PMID: 39072189; PMCID: PMC11273218.

Dehner CA, Johnson EF, Wieland CN, Camilleri MJ, Kajdacsy-Balla A, Oliveira AM, Halling KC, Gupta S, Guo R. J Cutan Pathol. 2024 Jul;51(7):538-548. doi: 10.1111/cup.14610. Epub 2024 Mar 31. PMID: 38556256.

June

Kircher BK, McCown MA, Scully DM, Behringer RR, Larina IV. Structural analysis of the female reptile reproductive system by micro-computed tomography and optical coherence tomography†. Biol Reprod. 2024 Jun 12;110(6):1077-1085. doi: 10.1093/biolre/ioae039. PMID: 38641547; PMCID: PMC11180613.

Xu J, Sun X, Chen Z, Ma H, Liu Y. Super-resolution imaging of T lymphocyte activation reveals chromatin decondensation and disrupted nuclear envelope. Commun Biol. 2024 Jun 10;7(1):717. doi: 10.1038/s42003-024-06393-1. PMID: 38858440; PMCID: PMC11164909.

Nguyen HT, Pietraszek N, Shelton SE, Arthur K, Kamm RD. J Biomed Opt. 2024 Jun;29(Suppl 2):S22710. doi: 10.1117/1.JBO.29.S2.S22710. Epub 2024 Aug 24. PMID: 39184400; PMCID: PMC11344342.

Liu Y, Uttam S. Perspective on quantitative phase imaging to improve precision cancer medicine. J Biomed Opt. 2024 Jun;29(Suppl 2):S22705. doi: 10.1117/1.JBO.29.S2.S22705. Epub 2024 Mar 26. PMID: 38584967; PMCID: PMC10996848.

De Niz M, Escobedo García R, Terán Ramirez C, Pakowski Y, Abonza Y, Bialy N, Orr VL, Olivera A, Abonza V, Alleva K, Allodi S, Almeida MF, Becerril Cuevas AR, Bonnet F, Burgos Solorio A, Chew TL, Chiabrando G, Cimini B, Cleret-Buhot A, Contreras Jiménez G, Daza L, De Sá V, De Val N, Delgado-Álvarez DL, Eliceiri K, Fiolka R, Grecco H, Hanein D, Hernández Herrera P, Hockberger P, Hernandez HO, Hernandez Guadarrama Y, Itano M, Jacobs CA, Jiménez-García LF, Jiménez Sabinina V, Kamaid A, Keppler A, Kumar A, Lacoste J, Lovy A, Luby-Phelps K, Mahadevan-Jansen A, Malacrida L, Mehta SB, Miller C, Miranda K, Moore JA, North A, O'Toole P, Olivares Urbano M, Pietrasanta LI, Portugal RV, Rossi AH, Sanchez Contreras J, Strambio-De-Castilla C, Soldevila G, Vale B, Vazquez D, Wood C, Brown CM, Guerrero A. J Microsc. 2024 Jun;294(3):420-439. doi: 10.1111/jmi.13318. Epub 2024 May 15. PMID: 38747464; PMCID: PMC11152921.

Hur SW, Kwon M, Manoharaan R, Mohammadi MH, Samuel AZ, Mulligan MP, Hergenrother PJ, Bhargava R. Capturing cell morphology dynamics with high temporal resolution using single-shot quantitative phase gradient imaging. J Biomed Opt. 2024 Jun;29(Suppl 2):S22712. doi: 10.1117/1.JBO.29.S2.S22712. Epub 2024 Jul 16. PMID: 39015510; PMCID: PMC11249975.

Goswami N, Anastasio MA, Popescu G. Quantitative phase imaging techniques for measuring scattering properties of cells and tissues: a review-part I. J Biomed Opt. 2024 Jun;29(Suppl 2):S22713. doi: 10.1117/1.JBO.29.S2.S22713. Epub 2024 Jul 18. PMID: 39026612; PMCID: PMC11257415.

Goswami N, Anastasio MA, Popescu G. Quantitative phase imaging techniques for measuring scattering properties of cells and tissues: a review-part II. J Biomed Opt. 2024 Jun;29(Suppl 2):S22714. doi: 10.1117/1.JBO.29.S2.S22714. Epub 2024 Jul 27. PMID: 9070593; PMCID: PMC11283205.

Iyer RR, Žurauskas M, Rao Y, Chaney EJ, Boppart SA. Bichromatic tetraphasic full-field optical coherence microscopy. J Biomed Opt. 2024 Jun;29(Suppl 2):S22704. doi: 10.1117/1.JBO.29.S2.S22704. Epub 2024 Mar 25. PMID: 38584966; PMCID: PMC10996847.

Szulczewski JM, Yesilkoy F, Ulland TK, Bartels R, Millis BA, Boppart SA, Eliceiri KW. To label or not: the need for validation in label-free imaging. J Biomed Opt. 2024 Jun;29(Suppl 2):S22717. doi: 10.1117/1.JBO.29.S2.S22717. Epub 2024 Dec 20. PMID: 39711795; PMCID: PMC11660684.

May

Ma H, Chen M, Nguyen P, Liu Y. Toward drift-free high-throughput nanoscopy through adaptive intersection maximization. Sci Adv. 2024 May 24;10(21):eadm7765. doi: 10.1126/sciadv.adm7765. Epub 2024 May 23. PMID: 38781327; PMCID: PMC11114195.

Ghosh B, Chatterjee J, Paul RR, Acuña S, Lahiri P, Pal M, Mitra P, Agarwal K. Sci Rep. 2024 May 8;14(1):10524. doi: 10.1038/s41598-024-61178-0. PMID: 38719976; PMCID: PMC11078950.

Huang KY, Upadhyay G, Ahn Y, Sakakura M, Pagan-Diaz GJ, Cho Y, Weiss AC, Huang C, Mitchell JW, Li J, Tan Y, Deng YH, Ellis-Mohr A, Dou Z, Zhang X, Kang S, Chen Q, Sweedler JV, Im SG, Bashir R, Chung HJ, Popescu G, Gillette MU, Gazzola M, Kong H. Proc Natl Acad Sci U S A. 2024 May 7;121(19):e2313590121. doi: 10.1073/pnas.2313590121. Epub 2024 Apr 29. PMID: 38683978; PMCID: PMC11087749.

Sorrells JE, Yang L, Iyer RR, Chaney EJ, Renteria CA, Boppart SA. Opt Lett. 2024 May 1;49(9):2513-2516. doi: 10.1364/OL.521864. PMID: 38691757.

Sengupta S, Anastasio MA. IEEE Trans Med Imaging. 2024 May;43(5):1753-1765. doi: 10.1109/TMI.2023.3348699. Epub 2024 May 2. PMID: 38163307; PMCID: PMC11065575.

Heaton AR, Burkard NJ, Sondel PM, Skala MC. Biophotonics Discov. 2024 May;1(1):015004. doi: 10.1117/1.bios.1.1.015004. Epub 2024 May 20. PMID: 39011049; PMCID: PMC11247620.

Desa DE, Amitrano MJ, Murphy WL, Skala MC. Optical redox imaging to screen synthetic hydrogels for stem cell-derived cardiomyocyte differentiation and maturation. Biophotonics Discov. 2024 May;1(1):015002. doi: 10.1117/1.bios.1.1.015002. Epub 2024 May 20. PMID: 39036366; PMCID: PMC11258857.

March

Yang L, Iyer RR, Sorrells JE, Renteria CA, Boppart SA. Temporally optimized and spectrally shaped hyperspectral coherent anti-Stokes Raman scattering microscopy. Opt Express. 2024 Mar 25;32(7):11474-11490. doi: 10.1364/OE.517417. PMID: 38570994; PMCID: PMC11021045.

De la Cadena A, Park J, Tehrani KF, Renteria CA, Monroy G, Boppart SA. Robust supercontinuum generation using an yttrium aluminum garnet crystal for multimodal label-free multiphoton microscopy. InLabel-free Biomedical Imaging and Sensing (LBIS) 2024 2024 Mar 13 (p. PC128540N). SPIE.

Sorrells JE, Park J, Aksamitiene E, Marjanovic M, Martin EM, Chaney EJ, Higham AM, Cradock KA, Liu ZG, Boppart SA. Label-free nonlinear optical signatures of extracellular vesicles in liquid and tissue biopsies of human breast cancer. Sci Rep. 2024 Mar 6;14(1):5528. doi: 10.1038/s41598-024-55781-4. PMID: 38448508; PMCID: PMC10917806.

Goswami N, Winston N, Choi W, Lai NZE, Arcanjo RB, Chen X, Sobh N, Nowak RA, Anastasio MA, Popescu G. EVATOM: an optical, label-free, machine learning assisted embryo health assessment tool. Commun Biol. 2024 Mar 5;7(1):268. doi: 10.1038/s42003-024-05960-w. PMID: 38443460; PMCID: PMC10915136.

Iyer RR, Sorrells JE, Tan KKD, Yang L, Wang G, Tu H, Boppart SA. Analog multiplexing of a laser clock and computational photon counting for fast fluorescence lifetime imaging microscopy. Biomed Opt Express. 2024 Mar 4;15(4):2048-2062. doi: 10.1364/BOE.514813. PMID: 38633095; PMCID: PMC11019682.

Clark GG, Geisler D, Coey EJ, Pollitz LJ, Zaki FR, Huang C, Boppart SA, Nguyen TH. Influence of phosphate on bacterial release from activated carbon point-of-use filters and on biofilm characteristics. Sci Total Environ. 2024 Mar 1;914:169932. doi: 10.1016/j.scitotenv.2024.169932. Epub 2024 Jan 8. PMID: 38199359.

Zhang C, Zaki FR, Won J, Boppart SA. A multimodal nonlinear optical microscopy study of the responses of Pseudomonas aeruginosa to blue light and antibiotic treatment. J Biophotonics. 2024 Mar;17(3):e202300384. doi: 10.1002/jbio.202300384. Epub 2023 Dec 15. PMID: 38010357; PMCID: PMC10961202.

Wang G, Boppart SA, Tu H. Compact simultaneous label-free autofluorescence multi-harmonic microscopy for user-friendly photodamage-monitored imaging. J Biomed Opt. 2024 Mar;29(3):036501. doi: 10.1117/1.JBO.29.3.036501. Epub 2024 Mar 14. PMID: 38487259; PMCID: PMC10939229.

February

Salirrosas O, Kawahara W, Vega EA, Bhargava R, Salehi O, Conrad C. ASO author reflections: Lymph node station 16 status-becoming a student of your patients' cancer. Ann Surg Oncol. 2024 Feb 29. doi: 10.1245/s10434-024-15099-x. Epub ahead of print. PMID: 38424261.

Arora G, Butola A, Rajput R, Agarwal R, Agarwal K, Horsch A, Prasad DK, Senthilkumaran P. Opt Express. 2024 Feb 26;32(5):7404-7416. doi: 10.1364/OE.512409. PMID: 38439421.

Bera K, Rojas-Gómez RA, Mukherjee P, Snyder CE, Aksamitiene E, Alex A, Spillman DR Jr, Marjanovic M, Shabana A, Johnson R, Hood SR, Boppart SA. Probing delivery of a lipid nanoparticle encapsulated self-amplifying mRNA vaccine using coherent Raman microscopy and multiphoton imaging. Sci Rep. 2024 Feb 22;14(1):4348. doi: 10.1038/s41598-024-54697-3. PMID: 38388635; PMCID: PMC10884293.

Chen J, Laverty DJ, Talele S, Bale A, Carlson BL, Porath KA, Bakken KK, Burgenske DM, Decker PA, Vaubel RA, Eckel-Passow JE, Bhargava R, Lou Z, Hamerlik P, Harley B, Elmquist WF, Nagel ZD, Gupta SK, Sarkaria JN. Aberrant ATM signaling and homology-directed DNA repair as a vulnerability of p53-mutant GBM to AZD1390-mediated radiosensitization. Sci Transl Med. 2024 Feb 14;16(734):eadj5962. doi: 10.1126/scitranslmed.adj5962. Epub 2024 Feb 14. PMID: 38354228.

January

Zhao R, Peng X, Kelkar VA, Anastasio MA, Lam F. High-dimensional MR reconstruction integrating subspace and adaptive generative models. IEEE Trans Biomed Eng. 2024 Jan 24;PP. doi: 10.1109/TBME.2024.3358223. Epub ahead of print. PMID: 38265912.

Zakomirnyi VI, Moroz A, Bhargava R, Rasskazov IL. Large fluorescence enhancement via lossless all-dielectric spherical mesocavities. ACS Nano. 2024 Jan 16;18(2):1621-1628. doi: 10.1021/acsnano.3c09777. Epub 2023 Dec 29. PMID: 38157441.

De la Cadena A, Park J, Tehrani KF, Renteria CA, Monroy GL, Boppart SA. Simultaneous label-free autofluorescence multi-harmonic microscopy driven by the supercontinuum generated from a bulk nonlinear crystal. Biomed Opt Express. 2024 Jan 2;15(2):491-505. doi: 10.1364/BOE.504832. PMID: 38404303; PMCID: PMC10890845.

Ran J, El-Kebir H, Lee Y, Chamorro LP, Berlin R, Aguiluz Cornejo GM, Benedetti E, Giulianotti PC, Bhargava R, Bentsman J, Ostoja-Starzewski M. Heat conduction in live tissue during radiofrequency electrosurgery. J R Soc Interface. 2024 Jan;21(210):20230420. doi: 10.1098/rsif.2023.0420. Epub 2024 Jan 17. PMID: 38228182; PMCID: PMC10791539.

Cam RM, Wang C, Thompson W, Ermilov SA, Anastasio MA, Villa U. Spatiotemporal image reconstruction to enable high-frame-rate dynamic photoacoustic tomography with rotating-gantry volumetric imagers. J Biomed Opt. 2024 Jan;29(Suppl 1):S11516. doi: 10.1117/1.JBO.29.S1.S11516. Epub 2024 Jan 19. PMID: 38249994; PMCID: PMC10798269.

Date unspecified

Yang L, Iyer RR, Sorrells JE, Chaney EJ, Boppart SA. Label-free multimodal polarization-sensitive optical microscope for multiparametric quantitative characterization of collagen. Optica, 11:155-165, 2024.

Iyer RR, Sorrells JE, Yang L, Renteria CA, Chaney EJ, Tehrani KF, Spillman DR Jr, Boppart SA. Exploring the structure, metabolism, and biochemistry of the neuronal microenvironment label-free using fast simultaneous multimodal optical microscopy. Optica, 11:1352-1367, 2024.

2023

December

Zhou W, Villa U, Anastasio MA. Ideal observer computation by use of Markov-chain Monte Carlo with generative adversarial networks. IEEE Trans Med Imaging. 2023 Dec;42(12):3715-3724. doi: 10.1109/TMI.2023.3304907. Epub 2023 Nov 30. PMID: 37578916; PMCID: PMC10769588.

Shaked NT, Boppart SA, Wang LV, Popp J. Label-free biomedical optical imaging. Nat Photonics. 2023 Dec;17(12):1031-1041. doi: 10.1038/s41566-023-01299-6. Epub 2023 Nov 16. PMID: 38523771; PMCID: PMC10956740.

November

Barya P, Xiong Y, Shepherd S, Gupta R, Akin LD, Tibbs J, Lee H, Singamaneni S, Cunningham BT. Photonic-plasmonic coupling enhanced fluorescence enabling digital-resolution ultrasensitive protein detection. Small. 2023 Nov;19(44):e2207239. doi: 10.1002/smll.202207239. Epub 2023 Apr 27. PMID: 37104850; PMCID: PMC10603207.

October

Zaki FR, Monroy GL, Shi J, Sudhir K, Boppart SA. Texture-based speciation of otitis media-related bacterial biofilms from optical coherence tomography images using supervised classification. Res Sq [Preprint]. 2023 Oct 26:rs.3.rs-3466690. doi: 10.21203/rs.3.rs-3466690/v1. PMID: 37961282; PMCID: PMC10635317.

Xia Q, Guo Z, Zong H, Seitz S, Yurdakul C, Ünlü MS, Wang L, Connor JH, Cheng JX. Single virus fingerprinting by widefield interferometric defocus-enhanced mid-infrared photothermal microscopy. Nat Commun. 2023 Oct 20;14(1):6655. doi: 10.1038/s41467-023-42439-4. PMID: 37863905; PMCID: PMC10589364.

Holcombe B, Foes A, Banerjee S, Yeh K, Wang SJ, Bhargava R, Ghosh A. Intermediate antiparallel β structure in amyloid β plaques revealed by infrared spectroscopic imaging. ACS Chem Neurosci. 2023 Oct 18;14(20):3794-3803. doi: 10.1021/acschemneuro.3c00400. Epub 2023 Oct 6. PMID: 37800883; PMCID: PMC10662787.

Spencer-Dene B, Mukherjee P, Alex A, Bera K, Tseng WJ, Shi J, Chaney EJ, Spillman DR Jr, Marjanovic M, Miranda E, Boppart SA, Hood SR. Localization of unlabeled bepirovirsen antisense oligonucleotide in murine tissues using in situ hybridization and CARS imaging. RNA. 2023 Oct;29(10):1575-1590. doi: 10.1261/rna.079699.123. Epub 2023 Jul 17. PMID: 37460153; PMCID: PMC10578491.

You Q, Lowerison MR, Shin Y, Chen X, Sekaran NVC, Dong Z, Llano DA, Anastasio MA, Song P. Contrast-free super-resolution power doppler (CS-PD) based on deep neural networks. IEEE Trans Ultrason Ferroelectr Freq Control. 2023 Oct;70(10):1355-1368. doi: 10.1109/TUFFC.2023.3304527. Epub 2023 Oct 17. PMID: 37566494; PMCID: PMC10619974.

Li F, Villa U, Duric N, Anastasio MA. A forward model incorporating elevation-focused transducer properties for 3-D full-waveform inversion in ultrasound computed tomography. IEEE Trans Ultrason Ferroelectr Freq Control. 2023 Oct;70(10):1339-1354. doi: 10.1109/TUFFC.2023.3313549. Epub 2023 Oct 17. PMID: 37682648; PMCID: PMC10775680.

September

Park J, Sorrells JE, Chaney EJ, Abdelrahman AM, Yonkus JA, Leiting JL, Nelson H, Harrington JJ, Aksamitiene E, Marjanovic M, Groves PD, Bushell C, Truty MJ, Boppart SA. In vivo label-free optical signatures of chemotherapy response in human pancreatic ductal adenocarcinoma patient-derived xenografts. Commun Biol. 2023 Sep 25;6(1):980. doi: 10.1038/s42003-023-05368-y. PMID: 37749184; PMCID: PMC10520051.

Falahkheirkhah K, Mukherjee SS, Gupta S, Herrera-Hernandez L, McCarthy MR, Jimenez RE, Cheville JC, Bhargava R. Accelerating cancer histopathology workflows with chemical imaging and machine learning. Cancer Res Commun. 2023 Sep 18;3(9):1875-1887. doi: 10.1158/2767-9764.CRC-23-0226. PMID: 37772992; PMCID: PMC10506535.

Granstedt JL, Zhou W, Anastasio MA. Approximating the Hotelling observer with autoencoder-learned efficient channels for binary signal detection tasks. J Med Imaging (Bellingham). 2023 Sep;10(5):055501. doi: 10.1117/1.JMI.10.5.055501. Epub 2023 Sep 26. PMID: 37767114; PMCID: PMC10520791.

August

Lozenski L, Wang H, Li F, Anastasio MA, Wohlberg B, Lin Y, Villa U. Learned full waveform inversion incorporating task information for ultrasound computed tomography. ArXiv [Preprint]. 2023 Aug 30:arXiv:2308.16290v1. PMID: 37693178; PMCID: PMC10491310.

Yeh K, Sharma I, Falahkheirkhah K, Confer MP, Orr AC, Liu YT, Phal Y, Ho RJ, Mehta M, Bhargava A, Mei W, Cheng G, Cheville JC, Bhargava R. Infrared spectroscopic laser scanning confocal microscopy for whole-slide chemical imaging. Nat Commun. 2023 Aug 25;14(1):5215. doi: 10.1038/s41467-023-40740-w. PMID: 37626026; PMCID: PMC10457288.

Mukherjee SS, Bhargava R. Phasor representation approach for rapid exploratory analysis of large infrared spectroscopic imaging data sets. Anal Chem. 2023 Aug 1;95(30):11365-11374. doi: 10.1021/acs.analchem.3c01539. Epub 2023 Jul 17. PMID: 37458316.

July

Goswami N, Winston N, Choi W, Lai NZE, Arcanjo RB, Chen X, Sobh N, Nowak RA, Anastasio MA, Popescu G. Machine learning assisted health viability assay for mouse embryos with artificial confocal microscopy (ACM). bioRxiv [Preprint]. 2023 Jul 30:2023.07.30.550591. doi: 10.1101/2023.07.30.550591. PMID: 37547014; PMCID: PMC10402120.

Shi J, Bera K, Mukherjee P, Alex A, Chaney EJ, Spencer-Dene B, Majer J, Marjanovic M, Spillman DR Jr, Hood SR, Boppart SA. Weakly supervised identification and localization of drug fingerprints based on label-free hyperspectral CARS microscopy. Anal Chem. 2023 Jul 25;95(29):10957-10965. doi: 10.1021/acs.analchem.3c00979. Epub 2023 Jul 14. PMID: 37450658; PMCID: PMC10372874.

Bhargava R, Yeh K, Kenkel S. High-fidelity micro- and nano-scale infrared spectroscopic imaging. Microsc Microanal. 2023 Jul 22;29(Suppl 1):562. doi: 10.1093/micmic/ozad067.268. PMID: 37613310.

Tehrani KF, Park J, Chaney EJ, Tu H, Boppart SA. Nonlinear imaging histopathology: A pipeline to correlate gold-standard hematoxylin and eosin staining with modern nonlinear microscopy. IEEE J Sel Top Quantum Electron. 2023 Jul-Aug;29(4 Biophotonics):6800608. doi: 10.1109/jstqe.2022.3233523. Epub 2023 Jan 2. PMID: 37193134; PMCID: PMC10174331.

June

Zhao J, Jiang L, Matlock A, Xu Y, Zhu J, Zhu H, Tian L, Wolozin B, Cheng JX. Mid-infrared chemical imaging of intracellular tau fibrils using fluorescence-guided computational photothermal microscopy. Light Sci Appl. 2023 Jun 15;12(1):147. doi: 10.1038/s41377-023-01191-6. PMID: 37322011; PMCID: PMC10272128.

Bhargava R. Digital histopathology by infrared spectroscopic imaging. Annu Rev Anal Chem (Palo Alto Calif). 2023 Jun 14;16(1):205-230. doi: 10.1146/annurev-anchem-101422-090956. Epub 2023 Apr 17. PMID: 37068745; PMCID: PMC10408309.

Lee H, Wang W, Chauhan N, Xiong Y, Magazine N, Valdescruz O, Kim DY, Qiu T, Huang W, Wang X, Cunningham BT. Rapid detection of intact SARS-CoV-2 using designer DNA Nets and a pocket-size smartphone-linked fluorimeter. Biosens Bioelectron. 2023 Jun 1;229:115228. doi: 10.1016/j.bios.2023.115228. Epub 2023 Mar 16. PMID: 36963325; PMCID: PMC10019040.

Kelkar VA, Gotsis DS, Brooks FJ, Kc P, Myers KJ, Zeng R, Anastasio MA. Assessing the ability of generative adversarial networks to learn canonical medical image statistics. IEEE Trans Med Imaging. 2023 Jun;42(6):1799-1808. doi: 10.1109/TMI.2023.3241454. Epub 2023 Jun 1. PMID: 37022374; PMCID: PMC10314718.

Valera E, Kindratenko V, Jankelow AM, Heredia J, Kim AY, Cowell TW, Chen CL, White K, Han HS, Bashir R. Electrochemical point-of-care devices for the diagnosis of sepsis. Curr Opin Electrochem. 2023 Jun;39:101300. doi: 10.1016/j.coelec.2023.101300. Epub 2023 Apr 14. PMID: 37483649; PMCID: PMC10357885.

Won J, Monroy GL, Khampang P, Barkalifa R, Hong W, Chaney EJ, Aksamitiene E, Porter RG, Novak MA, Spillman DR Jr, Kerschner JE, Boppart SA. In Vivo optical characterization of middle ear effusions and biofilms during otitis media. J Assoc Res Otolaryngol. 2023 Jun;24(3):325-337. doi: 10.1007/s10162-023-00901-6. Epub 2023 May 30. PMID: 37253962; PMCID: PMC10335988.

Park S, Villa U, Li F, Cam RM, Oraevsky AA, Anastasio MA. Stochastic three-dimensional numerical phantoms to enable computational studies in quantitative optoacoustic computed tomography of breast cancer. J Biomed Opt. 2023 Jun;28(6):066002. doi: 10.1117/1.JBO.28.6.066002. Epub 2023 Jun 20. PMID: 37347003; PMCID: PMC10281048.

May

Ghosh B, Agarwal K. Viewing life without labels under optical microscopes. Commun Biol. 2023 May 25;6(1):559. doi: 10.1038/s42003-023-04934-8. PMID: 37231084; PMCID: PMC10212946.

Liu L, Tibbs J, Li N, Bacon A, Shepherd S, Lee H, Chauhan N, Demirci U, Wang X, Cunningham BT. A photonic resonator interferometric scattering microscope for label-free detection of nanometer-scale objects with digital precision in point-of-use environments. Biosens Bioelectron. 2023 May 15;228:115197. doi: 10.1016/j.bios.2023.115197. Epub 2023 Mar 6. PMID: 36905862; PMCID: PMC10072782.

Perpetuini D, Günal M, Chiou N, Koyejo S, Mathewson K, Low KA, Fabiani M, Gratton G, Chiarelli AM. Fast optical signals for real-time retinotopy and brain computer interface. Bioengineering (Basel). 2023 May 5;10(5):553. doi: 10.3390/bioengineering10050553. PMID: 37237623; PMCID: PMC10215195.

April

He Z, Zhang Y, Tong X, Li L, Wang LV. Quantum microscopy of cells at the Heisenberg limit. Nat Commun. 2023 Apr 28;14(1):2441. doi: 10.1038/s41467-023-38191-4. PMID: 37117176; PMCID: PMC10147633.

Wang X, Shepherd S, Li N, Che C, Song T, Xiong Y, Palm IR, Zhao B, Kohli M, Demirci U, Lu Y, Cunningham BT. A target recycling amplification process for the digital detection of exosomal microRNAs through photonic resonator absorption microscopy. Angew Chem Int Ed Engl. 2023 Apr 11;62(16):e202217932. doi: 10.1002/anie.202217932. Epub 2023 Mar 6. PMID: 36622783; PMCID: PMC10073263.

Deshpande R, Avachat A, Brooks FJ, Anastasio MA. Investigating the robustness of a deep learning-based method for quantitative phase retrieval from propagation-based x-ray phase contrast measurements under laboratory conditions. Phys Med Biol. 2023 Apr 3;68(8):10.1088/1361-6560/acc2aa. doi: 10.1088/1361-6560/acc2aa. PMID: 36889005; PMCID: PMC10405978.

Cheng Z, Li C, Khadria A, Zhang Y, Wang LV. High-gain and high-speed wavefront shaping through scattering media. Nat Photonics. 2023 Apr;17(4):299-305. doi: 10.1038/s41566-022-01142-4. Epub 2023 Jan 23. PMID: 37333511; PMCID: PMC10275582.

March

Xiong Y, Shepherd S, Tibbs J, Bacon A, Liu W, Akin LD, Ayupova T, Bhaskar S, Cunningham BT. Photonic crystal enhanced fluorescence: A review on design strategies and applications. Micromachines (Basel). 2023 Mar 17;14(3):668. doi: 10.3390/mi14030668. PMID: 36985075; PMCID: PMC10059769.

Choi H, Iyer RR, Renteria CA, Boppart SA. Phase-sensitive detection of anomalous diffusion dynamics in the neuronal membrane induced by ion channel gating. Phys Med Biol. 2023 Mar 13;68(6):065005. doi: 10.1088/1361-6560/acbf9c. PMID: 36848681; PMCID: PMC10010434.

Shi J, Tu H, Park J, Marjanovic M, Higham AM, Luckey NN, Cradock KA, Liu ZG, Boppart SA. Weakly supervised identification of microscopic human breast cancer-related optical signatures from normal-appearing breast tissue. Biomed Opt Express. 2023 Mar 2;14(4):1339-1354. doi: 10.1364/BOE.480687. PMID: 37078030; PMCID: PMC10110327.

Chen X, Kandel ME, He S, Hu C, Lee YJ, Sullivan K, Tracy G, Chung HJ, Kong HJ, Anastasio M, Popescu G. Artificial confocal microscopy for deep label-free imaging. Nat Photonics. 2023 Mar;17(3):250-258. doi: 10.1038/s41566-022-01140-6. Epub 2023 Jan 12. PMID: 37143962; PMCID: PMC10153546.

February

Zhou W, VanDuyne P, Zhang C, Liu Y, Riessen R, Barragan M, Rowitz BM, Teran-Garcia M, Boppart SA, Anakk S. Pathological bile acid concentrations in chronic cholestasis cause adipose mitochondrial defects. JHEP Rep. 2023 Feb 23;5(5):100714. doi: 10.1016/j.jhepr.2023.100714. PMID: 37122689; PMCID: PMC10133756.

Bacon A, Wang W, Lee H, Umrao S, Sinawang PD, Akin D, Khemtonglang K, Tan A, Hirshfield S, Demirci U, Wang X, Cunningham BT. Review of HIV self testing technologies and promising approaches for the next generation. Biosensors (Basel). 2023 Feb 20;13(2):298. doi: 10.3390/bios13020298. PMID: 36832064; PMCID: PMC9954708.

Hsieh PH, Phal Y, Prasanth KV, Bhargava R. Cell phase identification in a three-dimensional engineered tumor model by infrared spectroscopic imaging. Anal Chem. 2023 Feb 14;95(6):3349-3357. doi: 10.1021/acs.analchem.2c04554. Epub 2022 Dec 27. PMID: 36574385; PMCID: PMC10214899.

January

Lee J, Du X, Park J, Cui Q, Iyer RR, Boppart SA, Gao L. Tunable image-mapping optical coherence tomography. Biomed Opt Express. 2023 Jan 5;14(2):627-638. doi: 10.1364/BOE.477646. PMID: 36874489; PMCID: PMC9979679.

Huang C, Clark GG, Zaki FR, Won J, Ning R, Boppart SA, Elbanna AE, Nguyen TH. Effects of phosphate and silicate on stiffness and viscoelasticity of mature biofilms developed with simulated drinking water. Biofouling. 2023 Jan;39(1):36-46. doi: 10.1080/08927014.2023.2177538. Epub 2023 Feb 27. PMID: 36847486; PMCID: PMC10065970.

Falahkheirkhah K, Tiwari S, Yeh K, Gupta S, Herrera-Hernandez L, McCarthy MR, Jimenez RE, Cheville JC, Bhargava R. Deepfake histologic images for enhancing digital pathology. Lab Invest. 2023 Jan;103(1):100006. doi: 10.1016/j.labinv.2022.100006. PMID: 36748189; PMCID: PMC10457173.

Cao R, Zhao J, Li L, Du L, Zhang Y, Luo Y, Jiang L, Davis S, Zhou Q, de la Zerda A, Wang LV. Optical-resolution photoacoustic microscopy with a needle-shaped beam. Nat Photonics. 2023 Jan;17(1):89-95. doi: 10.1038/s41566-022-01112-w. Epub 2022 Dec 1. PMID: 38149029; PMCID: PMC10751030.

Sun Y, Tu H, Boppart SA. Nonlinear optical imaging by detection with optical parametric amplification (invited paper). J Innov Opt Health Sci. 2023 Jan;16(1):2245001. doi: 10.1142/s1793545822450018. Epub 2022 Nov 21. PMID: 37583790; PMCID: PMC10426456.

Date unspecified

Sharma SN, Marsh JW, Tsipursky MS, Boppart SA. Ratiometric analysis of in vivo optical coherence tomography retinal layer thicknesses for detection of changes in Alzheimer’s disease. Translational Biophotonics. 2023, 5(3-4), e202300003 doi: 10.1002/tbio.202300003

2022

November

Kenkel S, Gryka M, Chen L, Confer MP, Rao A, Robinson S, Prasanth KV, Bhargava R. Chemical imaging of cellular ultrastructure by null-deflection infrared spectroscopic measurements. Proc Natl Acad Sci U S A. 2022 Nov 22;119(47):e2210516119. doi: 10.1073/pnas.2210516119. Epub 2022 Nov 14. PMID: 36375054; PMCID: PMC9704695.

Fanous MJ, He S, Sengupta S, Tangella K, Sobh N, Anastasio MA, Popescu G. White blood cell detection, classification and analysis using phase imaging with computational specificity (PICS). Sci Rep. 2022 Nov 21;12(1):20043. doi: 10.1038/s41598-022-21250-z. PMID: 36414631; PMCID: PMC9681839.

September

Iyer RR, Renteria CA, Yang L, Sorrells JE, Park J, Sun L, Yu Z, Huang Y, Marjanovic M, Mirica LM, Boppart SA. Tracking the binding of multi-functional fluorescent tags for Alzheimer's disease using quantitative multiphoton microscopy. J Biophotonics. 2022 Sep;15(9):e202200105. doi: 10.1002/jbio.202200105. Epub 2022 Jun 24. PMID: 35686672; PMCID: PMC9728943.

June

Thota PN, Nasibli J, Kumar P, Sanaka MR, Chak A, Zhang X, Liu X, Uttam S, Liu Y. Prediction of neoplastic progression in Barrett's esophagus using nanoscale nuclear architecture mapping: a pilot study. Gastrointest Endosc. 2022 Jun;95(6):1239-1246. doi: 10.1016/j.gie.2022.01.007. Epub 2022 Jan 20. PMID: 35065946; PMCID: PMC9296222