Notebook
Publication write-ups, research updates, and technical notes.
What Claude Code did and didn't do
I built Transit Gap and this site with Claude Code.
Rules of intracellular organization
Notes from the latest Allen Hour talk: are peroxisomes and endosomes randomly distributed inside a human stem cell? Mostly not. Mostly something more interesting.
Are peroxisomes randomly distributed?
First scientific application of the modernized cellPACK: using rule-based packing to test whether peroxisomes in hiPS cells are randomly arranged, nuclear-biased, or membrane-biased.
A new mathematical framework for cellular organization
Our database of 200,000 cell images yields a new way to understand the interior design of human cells — published in Nature.
Bringing cellPACK out of the box
How we pulled the cellPACK packing engine out of proprietary 3D-animation software, made it open source, and connected it to the Simularium web viewer.
Simularium: sharing biological simulations as easily as a link
Our paper in Nature Methods — an interactive web viewer for spatiotemporal biological models, built to remove the friction between simulation and collaboration.
Data → knowledge: the visualization scientist's bet
Notes from a job talk. In every subdiscipline of biology, data is outstripping our ability to analyze it. What does it take to bridge the gap?
Communicating motion in static images
Cave paintings, Muybridge, Duchamp. The 4D cell visualization problem is an old one, and the lineage is more useful than the software.
Building one cell from many cells
Notes from a year of work on the Integrated Mitotic Stem Cell — how we turned fifteen separately-tagged cell lines into one 3D portrait of mitosis, and what showing it taught me.
Generating 3D meshes and ambient occlusion maps for three.js
A three-stage pipeline — UCSF Chimera, Cinema4D Python SDK, batch processing — for turning microscopy data into web-ready 3D assets.
How do white blood cells move in 3D environments?
A research write-up and interview about our work on fast-moving immune cells — using lattice light sheet microscopy and custom visualization tools.
A tool that brings molecular biology into focus
Notes on the Chemistry & Biology cover and the metaphor it set up — kinase substrate pairs, but also everything I've made since.