Software and data
- 2026
Biohub – Cell Tracking During Development · kaggle.com/competitions/biohub-cell-tracking-during-development
Kaggle competition, June 29 – September 29, 2026: tracking every cell, including divisions, through 3D time-lapse movies of developing zebrafish embryos. Organizer. - 2025CryoLens is a pre-trained generative model for particle analysis in cryo-electron tomography. Given a single particle, it reconstructs the structure, embeds it, and estimates its pose. It is a variational autoencoder …
- 2024
CZII CryoET Object Identification
The CZII CryoET Object Identification Challenge, hosted on Kaggle from November 2024 to February 2025, was a machine learning competition focused on automating the detection of protein complexes in cryo-electron … - 2024CellCanvas is a software tool for creating and working with geometric models of cellular architectures.
- 2024
copick · copick.github.io/copick
copick is a cross-platform API for collaborative work on cryo-electron tomography datasets. It provides standardized access to tomograms, picks, and segmentations across different storage backends—whether your data is … - 2022napari is a Python viewer for multi-dimensional images. I joined CZI’s napari team in 2022, where I made code contributions and served as tech lead. I was on napari’s steering council from 2023 to 2026. …
- 2020Album is a software tool for sharing scientific code and software early in the development process. The goal is accelerating the iterative development of scientific software between developers and users. Check out the …
- 2016
SciView · github.com/scenerygraphics/sciview
SciView is an ImageJ/FIJI plugin for 3D visualization of images and meshes. It uses scenery as a rendering backend and supports rendering to VR headsets via OpenVR. - 2013
brevis · github.com/brevis-us/brevis
brevis is an artificial life simulator written in Clojure, for agent-based models with 3D visualization. Released on Clojars and archived on Zenodo (doi:10.5281/zenodo.803520). - 2026
Physarum time-lapse dataset · data
24 time-lapse series of Physarum polycephalum growing among arrangements of oat flakes, released as OME-Zarr on Zenodo.
Other software
- 2026
lodstone · creator · Python
Progressive loading of multiscale spatial arrays. - 2025–2026
rstar-python · creator · Rust, Python
Python bindings for the rstar R*-tree spatial index. - 2024–2025
copick packages · co-creator · Python
copick-torch, copick-utils, copick-server, copick-mcp, napari-copick. - 2024
surforama · co-creator · Python
Surface-based exploration of volumetric data in napari. - 2022–2023
napari multiscale rendering prototype · creator · Python
Prototype of multiscale rendering for napari. - 2022–2026
napari-stable-diffusion · creator · Python
Stable Diffusion plugin for napari. - 2022–2026
napari-tyssue · creator · Python
napari plugin for the tyssue tissue simulator. - 2019–2020
Cx3D (SciView and SNT) · maintainer · Java
Cx3D modeling framework adapted for SciView and SNT. - 2018
circuit_morphogenesis · creator · MATLAB
Code for “A circuit basis for morphogenesis” (2016). - 2017–2019
fun.grn · creator · Clojure
Gene regulatory networks in Clojure. - 2017–2019
escalation-ipd · creator · Java
Code for “Escalation of memory length in finite populations” (2019). - 2017
spacetime-nor-gates · creator · Clojure
Analysis code for chemical NOR-gate recordings. - 2016
Tufts COMP 135 (Spring 2016) · creator
Course materials, Introduction to Machine Learning and Data Mining. - 2015–2022
FunImageJ · creator · Clojure
Lisp framework for ImageJ; paper in Bioinformatics 2018. - 2014–2017
brevis-swarm-feedback-control · creator · Clojure
Feedback control of evolving swarms, simulated with brevis. - 2014
brevis-swarm-environmental-variation · creator · Clojure
Swarm evolution under environmental variation, simulated with brevis. - 2013–2019
clj-random · creator · Clojure
Random number generators for Clojure; used by Clojush. - 2011–2013
Clojush · contributor · Clojure
PushGP in Clojure; contributed zipper-based autoconstruction.