Jakob Troidl
I am an AI Scientist at HHMI Janelia Research Campus, affiliated with the AI@HHMI initiative. I lead the MIA-AI project, which develops foundational datasets and models for microscopy image analysis, integrating self-supervised pre-training, multi-modal learning, and cross-scale reasoning in biological systems.
I hold a Ph.D. in Computer Science from Harvard University, advised by Hanspeter Pfister. During my PhD, I was as a visiting researcher in the Turaga Lab at HHMI Janelia and a Machine Learning Fellow at E11.bio. I received my M.Sc. and B.Sc. degrees in Computer Science from TU Wien, Austria, and am originally from Regensburg, Germany.
My research spans applied machine learning and data visualization, with a particular emphasis on connectomics. My work centers on the development of scalable, interactive visual analysis systems and representation learning methods for uncovering the structural organization of the brain.
news
| Mar 04, 2026 | 💬 I’ll attend the AI and Biology conference at EMBL and the Synapses at Scale workshop at COSYNE. |
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| Mar 04, 2026 | 📖 My PhD thesis Scaling Computational Connectomics is now available online. |
| Jan 26, 2026 | 📢 I started as an AI Scientist at HHMI’s Janelia Research Campus. |
| Nov 18, 2025 | 🎓 I defended my PhD. Here’s the recording. |
| Jul 25, 2025 | 📢 Three papers accepted to IEEE VIS 2025 and one paper accepted to MICCAI EMA! |
| Jun 06, 2025 | 💬 I presented our preprint on neuron shape reasoning at the Modeling and Analysis of Connectomes conference and at the Frontiers in NeuroAI symposium. |
| Apr 10, 2025 | 💬 CAVE is out in Nature Methods. Check the paper out here. |
| Mar 14, 2025 | 💬 I will join E11.bio this summer as a ML fellow to work on automated connectome proofreading. |
| Dec 21, 2024 | 💬 I gave a talk on automated connectome proofreading at E11.bio, TU Wien and Google Research. |
