Projects

A non-exhaustive index of open-source work — 30+ public repositories, 600+ commits in the last year, grouped by domain. Most are research code, some are tooling I built because I needed it and could not find an existing equivalent.

Diffuse Optical Tomography

• piglet-realtime — Real-time multi-wavelength HbO/HbR DOT reconstruction for neonatal brain imaging.
• diff-photon-transport — Differentiable Monte Carlo photon transport in JAX/PyTorch.
• diffusion-priors-dot — Diffusion posterior sampling priors for DOT inverse reconstruction.
• dot-test-time-compute — o1-style test-time compute scaling for DOT reconstruction.
• dot-eval-harness — Versioned evaluation suite for DOT reconstruction pipelines.
• dspy-dot-rag — DSPy + ColBERT RAG over the DOT and fNIRS literature.

Preclinical neuroimaging (piglet)

• synpig — Autonomous piglet brain extraction with SynthSeg-style domain randomization (Dice 0.9622 on 4-week piglet skull stripping).
• sam-synthseg-piglet — SAM2 + SynthSeg-style domain randomization for contrast-agnostic piglet brain segmentation.
• PigSeg — Piglet brain segmentation pipeline.
• PUMBA-Piglet — Piglet brain analysis pipeline.
• DL-PigletBrainExtraction — 2.5D deep learning skull-stripping pipeline (PigBET).

Interpretability and ML systems

• biosignal-interp — Sparse-autoencoder mechanistic interpretability on a tiny fNIRS transformer.
• MathforNeuro — Survey of mathematical frameworks in neuroimaging.

Research infrastructure

• iu-hpc-agent — Verified IU Big Red 200 / Quartz HPC reference for AI coding agents.
• research-os — arXiv watcher + DSPy classifier + Obsidian writer on cron.
• wandering — Long-running self-directed reading project with autonomous agent lanes.
• paper2kindle — Search academic papers and send them to your Kindle.

Agent tooling

• 3brown1blue — First-principles Manim skill for paper-explainer animations.
• claude-skills — 266 Claude Code skills organized by domain.
• reskill — Terminal companion that quizzes you on the code Claude is working on.
• phd-outreach — Personalized PhD lab outreach with WebSearch PI research and LaTeX cover letters.
• claude-llm-proxy — OpenAI-compatible local HTTP proxy for Claude Code.

Apps and utilities

• autolog — macOS ambient context capture syncing to an Obsidian knowledge graph.
• push-to-phone — Tappable URL notifications from your shell to your phone via ntfy.sh.
• clicky-improvements — Hardened fork of farzaa/clicky with structured tool-use, persistent memory, eval harness.
• webclone — Website cloning pipeline (Playwright + CDP + React + Framer Motion + GSAP).

Full list at github.com/AmitSubhash.