Kyle Harrington
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  • Recent & Upcoming Talks
    • Lessons learned from the Kaggle challenge (invited panel)
    • napari tutorial at DL@MBL 2024
    • Dr. Kyle Harrington: Top Five Artificial Life Papers of All Time
    • State of the Art in Machine Learning for Bioimage Analysis (invited)
  • Projects
    • CZII CryoET Object Identification
    • CellCanvas
    • album
    • SciView
    • brevis
  • Publications
    • Annotating CryoET Volumes: A Machine Learning Challenge
    • Open-source Tools for CryoET Particle Picking Machine Learning Competitions
    • Surforama: interactive exploration of volumetric data by leveraging 3D surfaces
    • Polarity-JaM: An image analysis toolbox for cell polarity, junction and morphology quantification
    • napari-imagej: ImageJ Ecosystem Access from napari
    • Single‐cell profiling and zebrafish avatars reveal LGALS1 as immunomodulating target in glioblastoma
    • A Connectome of the Male Drosophila Ventral Nerve Cord
    • Machine learning-based ozone and PM2.5 forecasting: Application to multiple AQS sites in the Pacific Northwest
    • RS-FISH: precise, interactive, fast, and scalable FISH spot detection
    • PyZebrascope: An Open-Source Platform for Brain-Wide Neural Activity Imaging in Zebrafish
    • Can fractal dimensions objectivize gastropod shell morphometrics? A case study from Lake Lugu (SW China)
    • Development of a Machine Learning Approach for Local-Scale Ozone Forecasting: Application to Kennewick, WA
    • Complex population dynamics in a spatial microbial ecosystem with Physarum polycephalum
    • SNT: a unifying toolbox for quantification of neuronal anatomy
    • Active perception during angiogenesis: filopodia speed up Notch selection of tip cells in silico and in vivo
    • Bionic Tracking: Using Eye Tracking to Track Biological Cells in Virtual Reality
    • Tales from the Trenches: Developing sciview, a new 3D viewer for the ImageJ community
    • scenery: Flexible Virtual Reality Visualization on the Java VM
    • Mouse retinal cell behaviour in space and time using light sheet fluorescence microscopy
    • A large pool of actively cycling progenitors orchestrates self-renewal and injury repair of an ectodermal appendage
    • Multi-sample SPIM image acquisition, processing and analysis of vascular growth in zebrafish
    • Neuromodulated Learning in Deep Neural Networks
    • FunImageJ: a Lisp framework for scientific image processing
    • Competitive Dynamics in Eco-evolutionary Genetically-regulated Swarms
    • Escalation of Memory Length in Finite Populations
    • Escalation of Memory Length in Finite Populations
    • Asymmetric division coordinates collective cell migration in angiogenesis
    • A circuit basis for morphogenesis
    • Configurable NOR gate arrays from Belousov-Zhabotinsky micro-droplets
    • Temporal modulation of collective cell behavior controls vascular network topology
    • Genetically-regulated Neuromodulation Facilitates Multi-Task Reinforcement Learning
    • Gene Regulatory Network Evolution Through Augmenting Topologies
    • Can active perception generate bistability? Heterogeneous collective dynamics and vascular patterning
    • Feedback Control of Evolving Swarms
    • The Resilience of a Swarm Ecosystem Under Environmental Variation
    • Coevolution in Hide and Seek: Camouflage and Vision
    • Eco-evolutionary dynamics of complex social strategies in microbial communities
    • Eco-evolutionary dynamics of complex social strategies in microbial communities
    • Robot Coverage Control by Neuromodulation
    • Computational Neuroecology of Communicated Somatic Markers
    • Autoconstructive Evolution for Structural Problems
    • Tag-Based Modularity in Tree-Based Genetic Programming
    • The Effects of Finite Populations and Selection on the Emergence of Signaling
    • The Effects of Tags on the Evolution of Honest Signaling
    • Imaging analysis of clock neurons: light buffers the wake-promoting effect of dopamine
    • Communicated Somatic Markers Benefit Both the Individual and the Species
    • Tag-Based Modules in Genetic Programming
    • What’s in an Evolved Name? The Evolution of Modularity via Tag-Based Reference
    • En Route to Signal Inversion in Chemical Computing
    • Emotions for Strategic Real-Time Systems
    • Adaptive Multi-modal Sensors
    • Teaching the Evolution of Behavior with SuperDuperWalker
    • Selection Songs: Evolutionary Music Computation
  • Teaching
    • napari Tutorial DL at MBL 2024
      • Course Overview
      • Course Content
    • Introduction to Machine Learning and Data Mining
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  • napari Tutorial DL at MBL 2024
  • Introduction to Machine Learning and Data Mining

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  • Course Overview
  • Course Content
Teaching
napari Tutorial DL at MBL 2024

napari Tutorial DL at MBL 2024

Course Overview

This course covers DL in napari for image analysis.

Course Content

Detailed slides, assignments, and project guidelines can be found on the workshop page.

For more information and resources, visit the workshop GitHub repository.

Last updated on Aug 27, 2024
Introduction to Machine Learning and Data Mining Jan 1, 2016 →

© 2025 Kyle Harrington. This work is licensed under CC BY NC ND 4.0

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