Publications

Journal Papers

1. A. Chen, S. Han, S. Lee, C. Fu, C. Yang, L. Wu, S. Winfree, K. W. Dunn, P. Salama, and E. J. Delp, "Distributed and Networked Analysis of Volumetric Image Data for Remote Collaboration of Microscopy Image Analysis," Jounal of Medical Imaging, Volume 12, Issue 2, Article number 024001, March 2025, DOI: 10.1117/1.JMI.12.2.024001

2. L. Wu, A. Chen, P. Salama, S. Winfree, K. W. Dunn, and E. J. Delp, "NISNet3D: Three-Dimensional Nuclear Synthesis and Instance Segmentation for Fluorescence Microscopy Images," Scientific Reports, Volume 13, Article number 9533, June 2023, DOI: 10.1038/s41598-023-36243-9

3. A. Chen, L. Wu, S. Winfree, K. W. Dunn, P. Salama, and E. J. Delp, "3D Ground Truth Annotations of Nuclei in 3D Microscopy Volumes," bioRxiv, September 2022, DOI: 10.1101/2022.09.26.509542

4. D. J. Ho, D. Mas Montserrat, C. Fu, P. Salama, K. W. Dunn, and E. J. Delp, "Sphere estimation network: three-dimensional nuclei detection of fluorescence microscopy images," Journal of Medical Imaging, vol.7, no. 4, pp. 044003, 2020, DOI: 110.1117/1.JMI.7.4.044003

5. K. W. Dunn, C. Fu, D. J. Ho, S. Lee, S. Han, P. Salama, and E. J. Delp, "DeepSynth: Three-dimensional nuclear segmentation of biological images using neural networks trained with synthetic data," Scientific Reports, Volume 9, Article number: 18295, December 2019. DOI: 10.1038/s41598-019-54244-5

6. N. J. Gadgil, P. Salama, K. W. Dunn, and E. J. Delp, "Segmentation of biological images containing multitarget labeling using the jelly filling framework," Journal of Medical Imaging, vol. 5, no. 4, pp. 044006-1-12, November 2018. DOI: 10.1117/1.JMI.5.4.044006

7. K. W. Dunn, K. S. Lorenz, P. Salama, and E. J. Delp, "IMART software for correction of motion artifacts in images collected in intravital microscopy," IntraVital, vol. 3, no. 1, pp. e28210-1-10, 2014. DOI: 10.4161/intv.28210, PMID: 26090271, PMCID: PMC4469201

8. K. S. Lorenz, P. Salama, K. W. Dunn, and E. J. Delp, "Digital Correction of Motion Artifacts in Microscopy Image Sequences Collected from Living Animals Using Rigid and Non-Rigid Registration," Journal of Microscopy, vol. 245, no. 2, pp. 148-160, February 2012. DOI: 10.1111/j.1365-2818.2011.03557.x, PMID: 22092443, PMCID: PMC3856233

9. R. G. Presson Jr, M. B. Brown, A. J. Fisher, R. M. Sandoval, K. W. Dunn, K. S. Lorenz, E. J. Delp, P. Salama, B. A. Molitoris, and I. Petrache, "Two-Photon Imaging within the Murine Thorax without Respiratory and Cardiac Motion Artifact," The American Journal of Pathology, vol. 179, no. 1, pp. 75-82, July 2011. DOI: 10.1016/j.ajpath.2011.03.048, PMID: 21703395, PMCID: PMC3123791

Conference Proceedings and Presentations

1. L. Wu, A. Chen, P. Salama, K. W. Dunn, S. Winfree, and E. J. Delp, "A Quantitative Metric of Confidence For Segmentation of Nuclei in Large Spatially Variable Image Volumes," Proceedings of the 2024 IEEE 26th International Workshop on Multimedia Signal Processing (MMSP), October 2024, West Lafayette, IN. DOI: 10.1109/MMSP61759.2024.10743616

2. A. Chen, L. Wu, S. Winfree, K. W. Dunn, P. Salama, and E. J. Delp, "UNETRIS: Transformer-based Nuclear Instance Segmentation For Three-dimensional Fluorescence Microscopy Images," Proceedings of the SPIE Conference on Medical Imaging, February 2024, San Diego, CA. DOI: 10.1117/12.3005440

3. L. Wu, A. Chen, P. Salama, K. W. Dunn, and E. J. Delp, "3D CentroidNet: Nuclei Centroid Detection With Vector Flow Voting," Proceedings of the IEEE International Conference on Image Processing (ICIP), October 2022, Bordeaux, France. DOI: 10.1101/2022.07.21.500996

4. L. Wu, A. Chen, P. Salama, K. W. Dunn, and E. J. Delp, "An Ensemble Learning and Slice Fusion Strategy for Three-Dimensional Nuclei Instance Segmentation," Proceedings of the Computer Vision for Microscopy Image Analysis (CVMI) Workshop at Computer Vision and Pattern Recognition (CVPR), June 2022, New Orleans, LA. DOI: 10.1101/2022.04.28.489938

5. L. Wu, S. Han, A. Chen, P. Salama, K. W. Dunn, and E. J. Delp, "RCNN-SliceNet: A Slice and Cluster Approach for Nuclei Centroid Detection in Three-Dimensional Fluorescence Microscopy Images," Proceedings of the Computer Vision for Microscopy Image Analysis (CVMI) Workshop at Computer Vision and Pattern Recognition (CVPR), June 2021, Nashville, TN. DOI: 10.1109/CVPRW53098.2021.00416

6. A. Chen, L. Wu, S. Han, P. Salama, K. W. Dunn, and E. J. Delp, "Three Dimensional Synthetic Non-ellipsoidal Nuclei Volume Generation Using Bezier Curves," Proceedings of the IEEE International Symposium on Biomedical Imaging (ISBI), April 2021, Nice, France. DOI: 10.1109/ISBI48211.2021.9434149

7. S. Han, S. Lee, A. Chen, C. Yang, P. Salama, K. W. Dunn, and E. J. Delp, "Three Dimensional Nuclei Segmentation and Classification of Fluorescence Microscopy Images," Proceedings of the IEEE International Symposium on Biomedical Imaging (ISBI), April 2020, Iowa City, Iowa. DOI: 10.1109/ISBI45749.2020.9098560

8. D. J. Ho, S. Han, C. Fu, P. Salama, K. W. Dunn, and E. J. Delp, "Center-Extraction-Based Three Dimensional Nuclei Instance Segmentation of Fluorescence Microscopy Images," Proceedings of the IEEE International Conference on Biomedical and Health Informatics (BHI), May 2019, Chicago, IL. DOI: 10.1109/BHI.2019.8834516

9. S. Lee, S. Han, P. Salama, K. W. Dunn, and E. J. Delp, "Three Dimensional Blind Image Deconvolution for Fluorescence Microscopy Using Generative Adversarial Networks," Proceedings of the IEEE International Symposium on Biomedical Imaging (ISBI), April 2019, Venice, Italy. DOI: 10.1109/ISBI.2019.8759250

10. S. Han, S. Lee, C. Fu, P. Salama, K. W. Dunn, and E. J. Delp, "Nuclei Counting in Microscopy Images with Three Dimensional Generative Adversarial Networks," Proceedings of the SPIE Conference on Medical Imaging, February 2019, San Diego, CA. DOI: 10.1117/12.2512591

11. C. Fu, S. Lee, D. J. Ho, S. Han, P. Salama, K. W. Dunn, and E. J. Delp, "Three Dimensional Fluorescence Microscopy Image Synthesis and Segmentation," Proceedings of the Computer Vision for Microscopy Image Analysis (CVMI) Workshop at Computer Vision and Pattern Recognition (CVPR), June 2018. DOI: 10.1109/CVPRW.2018.00298

12. D. J. Ho, C. Fu, P. Salama, K. W. Dunn, and E. J. Delp, "Nuclei Detection and Segmentation of Fluorescence Microscopy Images Using Three Dimensional Convolutional Neural Networks," Proceedings of the IEEE International Symposium on Biomedical Imaging (ISBI), April 2018, Washington, DC. DOI: 10.1109/ISBI.2018.8363606

13. S. Lee, C. Fu, P. Salama, K. W. Dunn, and E. J. Delp, "Tubule Segmentation of Fluorescence Microscopy Images Based on Convolutional Neural Networks with Inhomogeneity Correction," Proceedings of the IS&T International Symposium on Electronic Imaging, January 2018, Burlingame, CA. DOI: 10.2352/ISSN.2470-1173.2018.15.COIMG-199

14. D. J. Ho, C. Fu, P. Salama, K. W. Dunn, and E. J. Delp, "Nuclei Segmentation of Fluorescence Microscopy Images Using Three Dimensional Convolutional Neural Networks," Proceedings of the Computer Vision for Microscopy Image Analysis (CVMI) Workshop at Computer Vision and Pattern Recognition (CVPR), July 2017, Honolulu, HI. DOI: 10.1109/CVPRW.2017.116

15. C. Fu, D. J. Ho, S. Han, P. Salama, K. W. Dunn, and E. J. Delp, "Nuclei Segmentation of Fluorescence Microscopy Images Using Convolutional Neural Networks," Proceedings of the IEEE International Symposium on Biomedical Imaging (ISBI), April 2017, Melbourne, Australia. DOI: 10.1109/ISBI.2017.7950617

16. S. Lee, P. Salama, K. W. Dunn, and E. J. Delp, "Segmentation of Fluorescence Microscopy Images Using Three Dimensional Active Contours with Inhomogeneity Correction," Proceedings of the IEEE International Symposium on Biomedical Imaging (ISBI), April 2017, Melbourne, Australia. DOI: 10.1109/ISBI.2017.7950618

17. D. J. Ho, P. Salama, K. W. Dunn, and E. J. Delp, "Boundary Segmentation for Fluorescence Microscopy Using Steerable Filters," Proceedings of the SPIE Conference on Medical Imaging, February 2017, Orlando, FL. DOI: 10.1117/12.2254627

18. C. Fu, N. Gadgil, K. Tahboub, P. Salama, K. Dunn, and E. J. Delp, "Four Dimensional Image Registration for Intravital Microscopy," Proceedings of the Computer Vision for Microscopy Image Analysis (CVMI) Workshop at Computer Vision and Pattern Recognition (CVPR), July 2016, Las Vegas, NV. DOI: 10.1109/CVPRW.2016.175

19. N. Gadgil, P. Salama, K. W. Dunn, and E. J. Delp, "Jelly Filling Segmentation of Fluorescence Microscopy Images Containing Incomplete Labeling," Proceedings of the IEEE International Symposium on Biomedical Imaging (ISBI), April 2016, Prague, Czech Republic. DOI: 10.1109/ISBI.2016.7493324

20. N. Gadgil, P. Salama, K. W. Dunn, and E. J. Delp, "Nuclei Segmentation of Fluorescence Microscopy Images Based on Midpoint Analysis and Marked Point Process," Proceedings of the IEEE Southwest Symposium on Image Analysis and Interpretation (SSIAI), March 2016, Santa Fe, NM. DOI: 10.1109/SSIAI.2016.7459169

21. S. Lee, P. Salama, K. W. Dunn, and E. J. Delp, "Boundary Fitting Based Segmentation of Fluorescence Micropscopy Images," Proceedings of the SPIE/IS&T International Symposium on Electronic Imaging, February 2015, San Francisco, CA. DOI: 10.1117/12.2085417

22. K. S. Lorenz, P. Salama, K. W. Dunn, and E. J. Delp, "Three Dimensional Segmentation Of Fluorescence Microscopy Images Using Active Surfaces," Proceedings of the IEEE International Conference on Image Processing (ICIP), September 2013, Melbourne, Australia. DOI: 10.1109/ICIP.2013.6738238

23. K. S. Lorenz, P. Salama, K. W. Dunn, and E. J. Delp, "A Multi-Resolution Approach to Non-Rigid Registration of Microscopy Images," Proceedings of the IEEE International Symposium on Biomedical Imaging (ISBI), May 2012, Barcelona, Spain. DOI: 10.1109/10.1109/ISBI.2012.6235518

24. K. S. Lorenz, P. Salama, K. W. Dunn, and E. J. Delp, "Non-Rigid Registration of Multiphoton Microscopy Images Using B-Splines," Proceedings of the SPIE Conference on Medical Imaging, February 2011, Lake Buena Vista (Orlando), FL. DOI: 10.1117/12.878304

25. K. S. Lorenz, F. Serrano, P. Salama, and E. J. Delp, "Segmentation And Registration Based Analysis Of Microscopy Images," Proceedings of the IEEE International Conference on Image Processing (ICIP), November 2009, Cairo, Egypt. DOI: 10.1109/ICIP.2009.5413531

26. K. S. Lorenz, F. Serrano, P. Salama, and E. J. Delp, "Analysis of Multiphoton Renal and Liver Microscopy Images: Preliminary Approaches to Segmentation and Registration," Proceedings of the 4th Workshop on Microscopic Image Analysis with Applications in Biology (MIAAB), September 2009, National Library of Medicine (NIH), Bethesda, MD.

Thesis

1. L. Wu, “Three-Dimensional Fluorescence Microscopy Image Synthesis And Analysis Using Machine Learning,” Ph.D. thesis at Purdue University, May 2023.

2. S. Han, “Fluorescence Microscopy Images Segmentation And Analysis Using Machine Learning,” Ph.D. thesis at Purdue University, August 2020.

3. S. Lee, “Segmentation And Deconvolution Of Fluorescence Microscopy Volumes,” Ph.D. thesis at Purdue University, August 2019.

4. D. J. Ho, “Three Dimensional Segmentation And Detection Of Fluorescence Microscopy Images,” Ph.D. thesis at Purdue University, May 2019.

5. C. Fu, “Microscopy Image Registration, Synthesis And Segmentation,” Ph.D. thesis at Purdue University, May 2019.

6. N. Gadgil, “Error Resilient Video Coding Using Bitstream Syntax And Iterative Microscopy Image Segmentation,” Ph.D. thesis at Purdue University, August 2016.

7. K. S. Lorenz, “Registration And Segmentation Based Analysis Of Microscopy Images,” Ph.D. thesis at Purdue University, May 2012.