Thomas Havlik

Software Architect | Medical Student

I'm a medical student pursuing pathology and a software architect with 15+ years of engineering experience. I build systems at the intersection of medicine, AI, and infrastructure.

Interested in computational pathology or medical AI? Let's talk.

Projects

13 records: systems, research, and infrastructure

EOV

Open source

A lightweight WSI viewer

A cross-platform desktop viewer for Whole-Slide Images, designed to make gigapixel histology slides easy to explore locally. EOV's approach is a lightweight, offline-first viewer that launches quickly and runs across operating systems without complex setup. Windows, macOS, and Linux are all supported.

Stack
rust, slint, vulkan

Eosin

Open source

WSI workbench for computational pathology

A collaborative Whole-Slide Imaging (WSI) platform built for computational pathology. The foundational project of the Eosin Platform, Eosin's scope is intentionally pure: ultra-high-performance, institution-grade WSI infrastructure.

Stack
rust, svelte, postgres, nats jetstream, kubernetes

HistoVAE

Open source
HistoVAE thumbnail

Fast-converging β-VAE for histopathology

A high-performance variational autoencoder for whole-slide histopathology images. HistoVAE trains on WSI tiles and converges both reliably and quickly enough to support real-time training and human-in-the-loop analysis. The project is open source and pre-trained models are available for immediate use.

Stack
python, tensorflow, pytorch, docker

cyto

Open source

Infrastructure for biological data

An early-stage platform for biomedical analysis, with target applications in bioinformatics, biochemistry, and computational pathology. Cyto focuses on providing a modern and general-purpose infrastructure layer for biological data. Auxiliary tools (oligonucleotide designer and a multisequence alignment analyzer) reflect its origins in the wet lab.

Stack
go, rust, python, flutter, postgres, kubernetes

Synapse

Closed source

LMS for medical curricula (working title)

An institution-scale Learning Management System (LMS) designed for medical curricula. Synapse leverages content-aware AI assistance to support both in-person and remote education. Tooling layers enforce answer correctness via formal logic and OpenEvidence-like RAG, which yields direct citations into the curriculum.

Stack
rust, lean, prolog, flutter, svelte, nats jetstream, postgres, kubernetes
Source
Closed. Media, details, and a demo are available on request.

seer

Closed source
seer thumbnail

Hybrid neural/keyword search engine

A multimodal search engine that blends neural and "old school" keyword approaches for robustness, predictability, and controllable retrieval. Seer specializes in the full spectrum of medical school curriculum assets: slideshows, PDFs, videos, images, Anki decks, and more. Designed for use by both humans and AI agents. Serves as the principal search backend for Synapse.

Stack
rust, nats jetstream, postgres
Source
Closed. Media, details, and a demo are available on request.

beebs.dev

Community
Beebles Laboratorium thumbnail

Open-source software lab

An open-source research and collaborative engineering lab I founded to explore medical AI, educational software, and creative computing. Now a community of 270+ members, Beebles Laboratorium coordinates numerous projects built on shared, enterprise-grade infrastructure. Current initiatives span scientific computing, language-learning platforms, and interactive media.

Stack
python, go, rust, kubernetes

Lyfe

Open source
lyfe thumbnail

2D molecular cell biology simulator

A GPU-accelerated molecular cell biology sandbox that explores how transport, thermodynamics, and reaction rules interact in a living system. Lyfe runs chemical and thermal simulations on the GPU while a rule engine yields reaction directives for the next simulation step. This project represents R&D for a video game idea I've had for over a decade, where players direct the evolution of life at the cellular level.

Stack
rust, lean, vulkan

TesseraDB

Open source

Soft real-time vector DB engine

A high-performance vector database engine that treats geometry as a first-class concept. TesseraDB emphasizes explicit topology so that spatial relationships are queryable, interpretable, and stable under incremental updates. Its core algorithms are built around topology-aware neighborhoods with optimization layers that ensure that query and update performance remain within soft real-time constraints.

Stack
zig

gib.gg

Open source
gib.gg logo

Multiplayer Doom in the browser

A massively scalable platform for playing custom Doom, solo or with friends, directly in the browser. gib.gg pairs a comprehensive WAD Browser for a multi-terabyte community content library with game services and distributed infrastructure to coordinate matchmaking, session management, and content delivery. Source code is open, the experience is frictionless, and no account is required.

Stack
c, svelte, nats jetstream, kubernetes

strim

Open source
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Live stream ingest and syndication

Distributed, fault-tolerant live stream syndication infrastructure designed around real operational requirements: resilient ingest, horizontal scale-out, and clear primitives for orchestration and recovery. Strim provides the core building blocks for platforms like Synapse and gib.gg, handling RTMP ingest, H.264 transcoding, HLS segment generation, and coordinated CDN storage.

Stack
rust, ffmpeg, kubernetes

e-Shadow

Open source
e-Shadowing Transcriber thumbnail

Live transcription for remote shadowing

A proof-of-concept platform integrating real-time transcription, medically aware NLP, and automatic reference retrieval to enhance remote physician shadowing. Built during the COVID-19 pandemic to improve remote shadowing experiences, it demonstrates an end-to-end pipeline from live audio to structured educational scaffolding using Go, Flutter, and Kubernetes-backed services.

Stack
go, flutter, kubernetes

AI portfolio

Open source
Machine learning portfolio banner

Medical ML projects, 2020 onward

A collection of machine learning projects spanning time series analysis, computer vision, NLP, and classical ML. This foundational work shaped my focus on medical AI and large-scale systems.

First commit: 21 November 2020.

Stack
python, pytorch, docker