Image Reconstruction of Multiphoton Microscopy Data. - Jared Doot; Kevin W. Eliceiri; Robert D. Nowak; Rebecca Willett (ISBI, 2009)

Unifying Biological Image Formats with HDF5. - Matthew T. Dougherty; Michael J. Folk; Erez Zadok; Herbert J. Bernstein; Frances C. Bernstein; Kevin W. Eliceiri; Werner Benger; Christoph Best (ACM Queue, 2009)

Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software. - Lee Kamentsky; Thouis R. Jones; Adam Fraser; Mark-Anthony Bray; David J. Logan; Katherine L. Madden; Vebjorn Ljosa; Curtis Rueden; Kevin W. Eliceiri; Anne E. Carpenter (Bioinform., 2011)

A chronic window imaging device for the investigation of in vivo peripheral nerves. - Sarah K. Brodnick; Mohammed R. Hayat; Sahil Kapur; Thomas J. Richner; Michael W. Nonte; Kevin W. Eliceiri; Lisa Krugner-Higby; Justin C. Williams; Samuel O. Poore (EMBC, 2014)

Closed-Loop Optogenetic Brain Interface. - Ramin Pashaie; Ryan Baumgartner; Thomas J. Richner; Sarah K. Brodnick; Mehdi Azimipour; Kevin W. Eliceiri; Justin C. Williams (IEEE Trans. Biomed. Eng., 2015)

SCIFIO: an extensible framework to support scientific image formats. - Mark C. Hiner; Curtis Rueden; Kevin W. Eliceiri (BMC Bioinform., 2016)

Sonification of hyperspectral fluorescence microscopy datasets. - Aprameya Mysore; Andreas Velten; Kevin W. Eliceiri (F1000Research, 2016)

Trainable Weka Segmentation: a machine learning tool for microscopy pixel classification. - Ignacio Arganda-Carreras; Verena Kaynig; Curtis Rueden; Kevin W. Eliceiri; Johannes E. Schindelin; Albert Cardona; H. Sebastian Seung (Bioinform., 2017)

ImageJ-MATLAB: a bidirectional framework for scientific image analysis interoperability. - Mark C. Hiner; Curtis T. Rueden; Kevin W. Eliceiri (Bioinform., 2017)

ImageJ2: ImageJ for the next generation of scientific image data. - Curtis T. Rueden; Johannes E. Schindelin; Mark C. Hiner; Barry E. DeZonia; Alison E. Walter; Ellen T. Arena; Kevin W. Eliceiri (BMC Bioinform., 2017)

ImageJ2: ImageJ for the next generation of scientific image data. - Curtis T. Rueden; Johannes E. Schindelin; Mark C. Hiner; Barry E. DeZonia; Alison E. Walter; Kevin W. Eliceiri (CoRR, 2017)

Neighborhood regularized image superresolution for applications to microscopic imaging. - Lopamudra Mukherjee; Adib Keikhosravi; Kevin W. Eliceiri (ISBI, 2018)

FunImageJ: a Lisp framework for scientific image processing. - Kyle I. S. Harrington; Curtis T. Rueden; Kevin W. Eliceiri (Bioinform., 2018)

Automated and Robust Quantification of Colocalization in Dual-Color Fluorescence Microscopy: A Nonparametric Statistical Approach. - Shulei Wang; Ellen T. Arena; Kevin W. Eliceiri; Ming Yuan 001 (IEEE Trans. Image Process., 2018)

Shedding Light: Integrating Bioimaging Technologies into the Design of an Interactive Museum Exhibit. - Joyce Ma; Eyal Shahar; Kevin W. Eliceiri; Guneet Mehta; Kristina Yu (Conference on Designing Interactive Systems, 2019)

Spatially Adaptive Colocalization Analysis in Dual-Color Fluorescence Microscopy. - Shulei Wang; Ellen T. Arena; Jordan T. Becker; William M. Bement; Nathan M. Sherer; Kevin W. Eliceiri; Ming Yuan 001 (IEEE Trans. Image Process., 2019)

Coding Scheme Optimization for Fast Fluorescence Lifetime Imaging. - Jongho Lee 004; Jenu Varghese Chacko; Bing Dai; Syed Azer Reza; Abdul Kader Sagar; Kevin W. Eliceiri; Andreas Velten; Mohit Gupta 001 (ACM Trans. Graph., 2019)

Dual-stream Maximum Self-attention Multi-instance Learning. - Bin Li 064; Kevin W. Eliceiri (CoRR, 2020)

Integration of the ImageJ Ecosystem in KNIME Analytics Platform. - Christian Dietz; Curtis T. Rueden; Stefan Helfrich; Ellen T. A. Dobson; Martin Horn; Jan Eglinger; Edward L. Evans; Dalton T. McLean; Tatiana Novitskaya; William A. Ricke; Nathan M. Sherer; Andries Zijlstra; et al. (Frontiers Comput. Sci., 2020)

Dual-Stream Multiple Instance Learning Network for Whole Slide Image Classification With Self-Supervised Contrastive Learning. - Bin Li 064; Yin Li 003; Kevin W. Eliceiri (CVPR, 2021)

MAT: Processing In-Memory Acceleration for Long-Sequence Attention. - Minxuan Zhou; Yunhui Guo; Weihong Xu; Bin Li 064; Kevin W. Eliceiri; Tajana Rosing (DAC, 2021)

Developing open-source software for bioimage analysis: opportunities and challenges. - Florian Levet; Anne E. Carpenter; Kevin W. Eliceiri; Anna Kreshuk; Peter Bankhead; Robert Haase 001 (F1000Research, 2021)

Single image super-resolution for whole slide image using convolutional neural networks and self-supervised color normalization. - Bin Li 064; Adib Keikhosravi; Agnes G. Loeffler; Kevin W. Eliceiri (Medical Image Anal., 2021)

Hyperdimensional Imaging Contrast Using an Optical Fiber. - Jenu Varghese Chacko; Han Nim Lee; Wenxin Wu; Marisa S. Otegui; Kevin W. Eliceiri (Sensors, 2021)

Meeting in the Middle: Towards Successful Multidisciplinary Bioimage Analysis Collaboration. - Anjalie Schlaeppi; Wilson Adams; Robert Haase 001; Jan Huisken; Ryan B. Macdonald; Kevin W. Eliceiri; Elisabeth Kugler (Frontiers Bioinform., 2022)

A deep learning framework for classifying microglia activation state using morphology and intrinsic fluorescence lifetime data. - Lopamudra Mukherjee; Abdul Kader Sagar; Jonathan N. Ouellette; Jyoti J. Watters; Kevin W. Eliceiri (Frontiers Neuroinformatics, 2022)

Moving beyond the desktop: prospects for practical bioimage analysis via the web. - Wei Ouyang; Kevin W. Eliceiri; Beth A. Cimini (Frontiers Bioinform., 2023)

Real-time open-source FLIM analysis. - Kevin K. D. Tan; Mark A. Tsuchida; Jenu Varghese Chacko; Niklas A. Gahm; Kevin W. Eliceiri (Frontiers Bioinform., 2023)

Collagen fiber centerline tracking in fibrotic tissue via deep neural networks with variational autoencoder-based synthetic training data generation. - Hyojoon Park; Bin Li 064; Yuming Liu; Michael S. Nelson; Helen M. Wilson; Eftychios Sifakis; Kevin W. Eliceiri (Medical Image Anal., 2023)

SciJava Ops: an improved algorithms framework for Fiji and beyond. - Gabriel J. Selzer; Curtis T. Rueden; Mark C. Hiner; Edward L. Evans; David Kolb; Marcel Wiedenmann; Christian Birkhold; Tim-Oliver Buchholz; Stefan Helfrich; Brian Northan; Alison E. Walter; Johannes E. Schindelin; et al. (Frontiers Bioinform., 2024)

SAMJ: Fast Image Annotation on ImageJ/Fiji via Segment Anything Model. - Carlos Garcia-Lopez-de-Haro; Caterina Fuster-Barceló; Curtis T. Rueden; Jónathan Heras; Vladimír Ulman; Daniel Franco-Barranco; Adrián Inés; Kevin W. Eliceiri; Jean-Christophe Olivo-Marin; Jean-Yves Tinevez; Daniel Sage; Arrate Muñoz-Barrutia (CoRR, 2025)