Kyle Harrington

Threads

Papers, software, courses and talks per year, by topic. An item can count in more than one topic.

• Evolution and artificial life
• Machine learning and AI
• Gene regulatory networks and neuromodulation
• Cells, tissues and development
• Bioimaging and visualization

Selected papers

• 2026
  • The Massive Multimodal Biomedical Understanding Challenge Challenge proposal
• 2026
  • A generative AI framework for disease-specific lung microtissue bioengineering bioRxiv
• 2021
  • SNT: a unifying toolbox for quantification of neuronal anatomy Nature Methods, 18(4)
• 2018
  • Artificial Gene Regulatory Networks—A Review Artificial Life
• 2018
  • Evolving Differentiable Gene Regulatory Networks PPSN 2018 EvoML Workshop
• 2016
  • Temporal modulation of collective cell behavior controls vascular network topology eLife

All 76 publications →

Timeline

1. 2026

   Senior Staff AI/ML Research Scientist, Biohub

   softwareBiohub – Cell Tracking During Developmentlodstone

   • The Massive Multimodal Biomedical Understanding Challenge Challenge proposal
   • Lessons learned from a Kaggle challenge for particle picking in cryo-electron tomography Nat Methods
   • A multimodal perturbation atlas defines the phenotypic resolution of cellular morphology bioRxiv
   • copick: An open dataset interface and toolkit for collaborative annotation and analysis of cryo-electron tomography data Protein Sci
   • A generative AI framework for disease-specific lung microtissue bioengineering bioRxiv
2. 2025

   softwareCryoLensrstar-python

   • A realistic phantom dataset for benchmarking cryo-ET data annotation Nat Methods
   • Advancing Particle Identification in Cryo-Electron Tomograms with Deep Learning Microscopy and Microanalysis (M&M 2025 abstract)
   • Polarity-JaM: An image analysis toolbox for cell polarity, junction and morphology quantification Nat Commun

   talksvolumeEM Gordon Research ConferenceCZII CryoET Object Identification Workshop

3. 2024

   softwarecopickCZII CryoET Object IdentificationCellCanvascopick packagessurforama

   • Open-source Tools for CryoET Particle Picking Machine Learning Competitions MLSB 2024
   • Surforama: interactive exploration of volumetric data by leveraging 3D surfaces bioRxiv
   • A Connectome of the Male Drosophila Ventral Nerve Cord eLife (Reviewed Preprint)

   taughtDL@MBL: Deep Learning for Microscopy Image Analysis (Marine Biological Laboratory)

   talksDL@MBL 2024Last Monkey Standing chat

4. 2023
   • napari-imagej: ImageJ Ecosystem Access from napari Nature Methods, 20(10), 1443-1444
   • Single‐cell profiling and zebrafish avatars reveal LGALS1 as immunomodulating target in glioblastoma EMBO Molecular Medicine, 15(e18144)
   • State of the Art for Machine Learning in Bioimage Analysis Microscopy and Microanalysis (M&M 2023 abstract)
   • Machine learning-based ozone and PM2.5 forecasting: Application to multiple AQS sites in the Pacific Northwest Frontiers in Big Data, 6
   • Image Informatics Microscope Image Processing

   talksHalfway to I2K 2023Microscopy and Microanalysis 2023, MinneapolisMicroscopy and Microanalysis 2023, Minneapolisnapari Plugin Foundations Grant Showcase, CZI (virtual)

5. 2022

   softwarenaparinapari multiscale rendering prototypenapari-stable-diffusionnapari-tyssue

   • RS-FISH: precise, interactive, fast, and scalable FISH spot detection Nature Methods, 19(12)
   • PyZebrascope: An Open-Source Platform for Brain-Wide Neural Activity Imaging in Zebrafish Frontiers in Cell and Developmental Biology, 10
   • Can fractal dimensions objectivize gastropod shell morphometrics? A case study from Lake Lugu (SW China) Ecology and Evolution, 12(e8622)
   • Development of a Machine Learning Approach for Local-Scale Ozone Forecasting: Application to Kennewick, WA Front. Big Data
6. 2021

   Senior Researcher, Oak Ridge National Laboratory

   • Album: executable building blocks for scientific imaging routines, from sharing to LLM-assisted orchestration arXiv
   • Complex population dynamics in a spatial microbial ecosystem with Physarum polycephalum Biosystems, 208, 104483
   • SNT: a unifying toolbox for quantification of neuronal anatomy Nature Methods, 18(4)
   • Review of The Digital Cell: Cell Biology as a Data Science. By Stephen J. Royle The Quarterly Review of Biology, 96(1), 58–59
   • Active perception during angiogenesis: filopodia speed up Notch selection of tip cells in silico and in vivo Phil. Trans. R. Soc. B

   talksiNAMES Graduate Program, Max Delbrück Center, BerlinUltrahigh Field Magnetic Resonance Symposium, BerlinMax Delbrück Center, BerlinCenter for Advanced Systems Understanding (CASUS), GörlitzFOSDEM 2021, Kotlin devroom

7. 2020

   Group Leader, Image Data Analysis, Helmholtz Imaging Platform, Max Delbrueck Center for Molecular Medicine

   softwarealbum

   • Bionic Tracking: Using Eye Tracking to Track Biological Cells in Virtual Reality ECCV 2020 Workshops
   • Tales from the Trenches: Developing sciview, a new 3D viewer for the ImageJ community VisGap 2020
   • Mouse retinal cell behaviour in space and time using light sheet fluorescence microscopy eLife, 9

   talksI2K 2020J-theory, Janelia Research Campus, HHMI

8. 2019

   softwareCx3D (SciView and SNT)

   • scenery: Flexible Virtual Reality Visualization on the Java VM VIS 2019
   • A large pool of actively cycling progenitors orchestrates self-renewal and injury repair of an ectodermal appendage Nature Cell Biology, 21(9)
   • Escalation of Memory Length in Finite Populations Artificial Life
   • Multi-sample SPIM image acquisition, processing and analysis of vascular growth in zebrafish Development, 146(dev173757)

   talksCenter for Cell Analysis and Modeling Seminar, UConn, Farmington, CTJ-theory, Janelia Research Campus, HHMIImage-based Modeling and Simulation 2019

9. 2018

   softwarecircuit_morphogenesis

   • Neuromodulated Learning in Deep Neural Networks arXiv
   • Artificial Gene Regulatory Networks—A Review Artificial Life
   • Acquisition and reconstruction of 4D surfaces of axolotl embryos with the flipping stage robotic microscope Biosystems, 173, 214–220
   • Evolving Differentiable Gene Regulatory Networks PPSN 2018 EvoML Workshop
   • FunImageJ: a Lisp framework for scientific image processing Bioinformatics, 34(5), 899-900

   taughtCapstone (University of Idaho)

   talksWisconsin Institute for DiscoveryHHMI Collective Computation Conference

10. 2017

    softwarefun.grnescalation-ipdspacetime-nor-gates

    • Dynamic Habitat Construction Through Evolving 3D Swarms ECAL 2017 Living Architectures
    • Competitive Dynamics in Eco-evolutionary Genetically-regulated Swarms ECAL 2017

    taughtCapstone (University of Idaho)Artificial Life (University of Idaho)

    talksData Science Day, Washington State University, Pullman, WABosLab, Somerville, MAIBEST, University of Idaho, Moscow, IDMax Planck Institute of Molecular Cell Biology and Genetics, DresdenIRIT Symposium, University of Toulouse2IS Innovative Information Systems, University of ToulouseBEACON Institute, Michigan State University & University of Idaho2017 NIH IDeA Western Regional ConferenceImageXD, University of Washington, Seattle, WAMathematical Biology Seminar, Washington State University, Pullman, WA

11. 2016

    Assistant Professor, Virtual Technology and Design, University of Idaho

    softwareSciViewTufts COMP 135 (Spring 2016)

    • Asymmetric division coordinates collective cell migration in angiogenesis Nature Cell Biology, 18(12)
    • Review of Wolfgang Banzhaf and Lidia Yamamoto: Artificial Chemistries, MIT Press, 2015 Genetic Programming and Evolvable Machines, 17(3), 317–319
    • A circuit basis for morphogenesis Theoretical Computer Science, 633
    • Configurable NOR gate arrays from Belousov-Zhabotinsky micro-droplets European Physical Journal Special Topics, 225(1)
    • Temporal modulation of collective cell behavior controls vascular network topology eLife

    taughtIntroduction to Machine Learning and Data Mining (Tufts University)

    talksInstitute for Bioinformatics and Evolutionary Studies, University of IdahoLaboratory for Optical and Computational Instrumentation, University of Wisconsin, Madison, WICenter for Modeling Complex Interactions, University of IdahoIdaho EPSCoR Annual Meeting, Coeur d'Alene, ID

12. 2015

    softwareFunImageJ

    • Genetically-regulated Neuromodulation Facilitates Multi-Task Reinforcement Learning GECCO-2015
    • Gene Regulatory Network Evolution Through Augmenting Topologies IEEE Transactions on Evolutionary Computation, 19(6)
    • Functional Image Processing with ImageJ/FIJI BioImage Informatics 2015

    talksClojure/Conj 2015, Philadelphia, PABioimage Informatics 2015, NIST, Gaithersburg, MD

13. 2014

    Postdoctoral Fellow, Bentley Group, Beth Israel Deaconess Medical Center, Harvard Medical School

    softwarebrevis-swarm-feedback-controlbrevis-swarm-environmental-variation

    • Can active perception generate bistability? Heterogeneous collective dynamics and vascular patterning ALIFE 14
    • Feedback Control of Evolving Swarms ALIFE 14
    • The Resilience of a Swarm Ecosystem Under Environmental Variation ALIFE 14
    • Coevolution in Hide and Seek: Camouflage and Vision ALIFE 14
    • Modelling nonlinear chemical oscillators with inhibitory coupling NEBEC 2014
    • Eco-evolutionary dynamics of complex social strategies in microbial communities Communicative & Integrative Biology, 7(1)
    • Escalation of Coevolutionary Arms Races PhD thesis, Brandeis University

    talksHHMI Interfaces Award Lecture Series, Waltham, MAHHMI Interfaces Award Lecture Series, Waltham, MAALife 14, New York, NY

14. 2013

    softwarebrevisclj-random

    • Robot Coverage Control by Evolved Neuromodulation IJCNN-2013

    taughtArtificial Life (Brandeis University)Introduction to Computers (Brandeis University)

    talksIJCNN 2013, Dallas, TXQuantitative Biology Graduate Talks, Brandeis University

15. 2012
    • Computational Neuroecology of Communicated Somatic Markers Alife 2012
    • Tag-Based Modularity in Tree-Based Genetic Programming GECCO-2012
    • Autoconstructive Evolution for Structural Problems GECCO-2012 Companion
    • The Effects of Finite Populations and Selection on the Emergence of Signaling ALIFE 13
    • The Effects of Tags on the Evolution of Honest Signaling GECCO-2012 Companion

    taughtAutomated Speech Recognition (Brandeis University)Introduction to Scientific Computing (Brandeis University)

    talksGECCO 2012, Philadelphia, PA

16. 2011

    softwareClojush

    • Communicated Somatic Markers Benefit Both the Individual and the Species IJCNN-2011
    • Tag-Based Modules in Genetic Programming GECCO-2011
    • Fecundity and selectivity in evolutionary computation GECCO '11 Companion
    • What’s in an Evolved Name? The Evolution of Modularity via Tag-Based Reference GPTP IX
    • Imaging analysis of clock neurons reveals light buffers the wake-promoting effect of dopamine Nature Neuroscience, 14(7), 889–895
    • Computational Emotions Encourage Collective Behavior in Population Dynamics ICCS 2011
    • Compositional Autoconstructive Dynamics ICCS 2011

    taughtArtificial Life (Brandeis University)Fundamentals of Artificial Intelligence (Brandeis University)

    talksIJCNN 2011, San Jose, CAQuantitative Biology Graduate Talks, Brandeis UniversityALFA Group, MIT, Cambridge, MAICCS 2011, Quincy, MA

17. 2010
    • En Route to Signal Inversion in Chemical Computing ALIFE XII
    • Robot phylogenetics GECCO '10 Companion
    • Conspecific Emotional Cooperation Biases Population Dynamics: A Cellular Automata Approach International Journal of Natural Computing Research, 1(3), 51–65

    taughtTopics in Natural Language Processing: Speech Recognition (Brandeis University)

    talksGECCO 2010, Portland, ORBoston College, Boston, MA

18. 2009

    taughtMachine Learning (Brandeis University)

19. 2008

    Graduate Research and Teaching Assistant, DEMO Lab, Computer Science, Brandeis University

    • Emotions for Strategic Real-Time Systems AAAI Spring Symposium

    taughtComputer Science Projects (Hampshire College)Computer Programming in C and C++ (Hampshire College)

    talksGreythumb Artificial Life Group, Cambridge, MA

20. 2007

    Instructor of Computer Science, Hampshire College

    • Adaptive Multi-modal Sensors 50 Years of AI
    • Predicting reactions from amino acid sequences in S. cerevisiae: an evolutionary computation approach GECCO '07 Companion
    • Predicting reactions from amino acid sequences in S. cerevisiae: an evolutionary computation approach Undergraduate thesis, Hampshire College

    taughtData Structures (Hampshire College)Introduction to Algorithms (University of Massachusetts Amherst)

    talksGECCO 2007, London, UK

21. 2005
    • Teaching the Evolution of Behavior with SuperDuperWalker AIED 2005
    • Selection Songs: Evolutionary Music Computation YLEM Journal

Recent talks

• 2025 Understanding Cellular Architecture with Interactive Machine Learning (invited) volumeEM Gordon Research Conference
• 2025 Lessons learned from the Kaggle challenge (invited panel) CZII CryoET Object Identification Workshop
• 2024 napari tutorial DL@MBL 2024
• 2024 Top Five Artificial Life Papers of All Time Last Monkey Standing chat
• 2023 napari workshop Halfway to I2K 2023
• 2023 State of the Art in Machine Learning for Bioimage Analysis (invited) Microscopy and Microanalysis 2023, Minneapolis
• 2023 napari workshop Microscopy and Microanalysis 2023, Minneapolis
• 2023 What's next for napari? napari Plugin Foundations Grant Showcase, CZI (virtual)

All 50 talks →