Austin Lefebvre
Senior Data Scientist
San Francisco, California, United States
Summary
👤
Senior🎓
Top SchoolAustin Lefebvre is a Senior Data Scientist and NSF Graduate Research Fellow specializing in microscopy-driven machine learning and high-dimensional phenotypic analysis, currently building deep learning and GPU-accelerated pipelines at Calico Life Sciences. With 9–11 years of interdisciplinary research experience across R1 institutions, he blends representation learning (BYOL, GNN attention autoencoders, SWIN UNETRs) and scalable CUDA/PyTorch engineering to tackle 5D/whole-organ imaging, spatial transcriptomics, and live-cell phenotyping. He’s the creator of open-source tools like Nellie and Mitometer that make complex image analysis accessible to biologists, and he regularly publishes and presents methods bridging hypothesis generation to data interpretation. Trained as a biomedical engineer (PhD, UC Irvine) and experienced in hands-on cell handling and high-content experimental design, he uniquely translates wet-lab nuance into production-ready computational solutions.
9 years of coding experience
10 years of employment as a software developer
Bioengineering, Bioengineering at University of WashingtonWestlake HighschoolUniversity of California, IrvineUniversity of California, San DiegoSanta Barbara High School
English, French, matlab, python, latex, imagej
Github Skills (12)
segmentation10
image-processing9
microscopy9
feature-extraction9
image-analysis9
biology9
machine-learning8
3d8
conda3
python3
animation3
conda-forge2
Programming languages (2)
Github contributions (5)
aelefebv/nellie
Mar 2024 - May 2026
Nellie: Automated organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy
Contributions:49 PRs, 241 pushes, 111 branches in 2 years 2 months
3dfeature-extractionsegmentationbiologyfluorescence
aelefebv/Mitometer
Nov 2020 - Sep 2021
Automated mitochondrial segmentation and tracking.
Contributions:2 releases, 36 commits, 2 PRs in 9 months
segmentation
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