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 architecture? Let's talk.

Contact
Field 800 × 550 µm Nuclei — Regions 4 flagged Tiles 0 / 70
01 Discipline
Computational pathology Medical AI architecture
02 Clinical track
Medical student Pathology
03 Training
B.Sc. Chemistry Minor in Mathematics
04 Engineering
15+ years Professional experience
Latest from the blog Managing Time & Stress To follow up on a previous post and answer a question I get surprisingly often how I manage to get so much done I want to share a loose collection of ideas that I've found particularly helpful. Software engineering in 2026 comes with a uniquely demanding life… Read post →

Specimen index

Projects

S26-001 open source

Eosin

Next-generation WSI workbench

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.

  • rust
  • svelte
  • postgres
  • nats jetstream
  • kubernetes
S26-002 open source

EOV

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.

  • rust
  • slint
  • vulkan
S26-003 open source
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HistoVAE

Lightning fast 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.

  • python
  • tensorflow
  • pytorch
  • docker
S26-004 open source

cyto

Biomedical research at scale

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.

  • go
  • rust
  • python
  • flutter
  • postgres
  • kubernetes
S26-005 closed source

Synapse

AI-native LMS. 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.

  • rust
  • lean
  • prolog
  • flutter
  • svelte
  • nats jetstream
  • postgres
  • kubernetes

Closed-source project — media, details, and demo available on request.

S26-006 closed source
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seer

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.

  • rust
  • nats jetstream
  • postgres

Closed-source project — media, details, and demo available on request.

S26-007 community / ecosystem
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beebs.dev

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.

  • python
  • go
  • rust
  • kubernetes
S26-008 open source
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Lyfe

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.

  • rust
  • lean
  • vulkan
S26-009 open source

TesseraDB

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.

  • zig
S26-010 open source
gib.gg logo

gib.gg

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.

  • c
  • svelte
  • nats jetstream
  • kubernetes
S26-011 open source
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strim

Scalable live stream infrastructure

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.

  • rust
  • ffmpeg
  • kubernetes
S26-012 open source
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e-Shadow

Physician shadowing, enhanced.

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.

  • go
  • flutter
  • kubernetes
S26-013 open source
Machine learning portfolio banner

AI portfolio

Various medical AI implementations

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

First commit: 21 November 2020.

  • python
  • pytorch
  • docker
S26-014 Slot open

Next specimen

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