Jakob Troidl
I am an AI Scientist at HHMI Janelia, part of the AI@HHMI initiative, where I lead the MIA-AI project. We build large-scale datasets and pre-trained models for microscopy image analysis, using self-supervised and multi-modal learning and architectures that reason across spatial scales.
My background is in computer science and connectomics, the reconstruction and analysis of neural circuits from nanometer-resolution microscopy data. I’ve worked on learned models of neuron morphology and self-supervised isotropic volume reconstruction, proofreading and annotation infrastructure (CAVE, SynAnno), and tools for analyzing circuit motifs (Vimo, MoMo). I also contributed to the largest human connectome to date and a connectome of the larval zebrafish brain.
I received my Ph.D. in Computer Science from Harvard, advised by Hanspeter Pfister, with research stays in the Turaga Lab at Janelia and at E11.bio as an ML Fellow. I hold a B.Sc. and M.Sc. in computer science from TU Wien.
news
| Mar 04, 2026 | 🇸🇪 Keynote at the BIC workshop at ECCV in Malmö: Probing Scaling Laws in Microscopy Image Analysis. |
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| Mar 04, 2026 | 💬 Attending AI and Biology at EMBL and the Synapses at Scale workshop at COSYNE. |
| Mar 04, 2026 | 📖 My PhD thesis, Scaling Computational Connectomics, is online. |
| Jan 26, 2026 | 📢 Started as an AI Scientist at HHMI Janelia. |
| Nov 18, 2025 | 🎓 Defended my PhD (recording). |
| Jul 25, 2025 | 📢 Three papers accepted to IEEE VIS 2025 and one to MICCAI EMA! |
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| Jun 06, 2025 | 💬 Presented neuron shape reasoning at Analysis and Modeling of Connectomes and Frontiers in NeuroAI. |
| Apr 10, 2025 | 📝 CAVE is out in Nature Methods. |
| Mar 14, 2025 | 🔬 Joining E11.bio this summer as an ML Fellow on automated connectome proofreading. |
| Dec 21, 2024 | 💬 Talks on automated connectome proofreading at E11.bio, TU Wien, and Google Research. |
| Nov 24, 2024 | 📝 New preprint on automated connectome proofreading and typing with global neuron shape reasoning. |
| Oct 15, 2024 | 💬 Presented at the IEEE VIS Doctoral Colloquium (remote). |
| Jun 25, 2024 | 💬 Talk on neural implicit volume reconstruction at IST Austria. |
| Jun 23, 2024 | 💬 Talk on interactive motif analysis at the International Connectomics Conference in Berlin. |
| May 15, 2024 | 🧠 Started as a visiting researcher in the Turaga Lab at HHMI Janelia. |
| May 01, 2024 | 📝 New preprint on neural implicit isotropic volume reconstruction. |
| Feb 02, 2024 | 💬 Talk on human-centered computing in connectomics at Harvard Medical School. |
| Aug 02, 2023 | 📝 Vimo accepted to IEEE VIS 2023 🇦🇺. |
| May 21, 2022 | 📝 Two papers at EuroVis 2022: Barrio and a connectomics survey. |
| Jul 08, 2021 | 🎓 M.Sc. in Visual Computing from TU Wien (thesis). |
| Apr 15, 2021 | 🎉 Joining the Visual Computing Group at Harvard this fall for my Ph.D. |
| Aug 23, 2020 | 🏆 Best SciVis Paper at IEEE VIS 2020. |
| Jan 21, 2020 | 🎓 Among the first graduates of the TU Wien Informatics Bachelor with Honors program. |
