Jeremy Magland

Software

Selected open-source projects.

Screenshot of Numbl

Numbl

Open-source MATLAB-compatible computing environment that runs .m files in the browser and on the command line; early stage (with Dan Fortunato).

numbl.orgsource

Screenshot of mip

mip

Package manager for MATLAB and numbl: dependencies, precompiled MEX binaries, and path management; early stage (with Dan Fortunato).

mip.shsource

Screenshot of Neurosift

Neurosift

Browser-based visualization of NWB (Neurodata Without Borders) files and interactive exploration of the DANDI Archive, EMBER Archive, and OpenNeuro (with the CatalystNeuro team).

neurosift.appsourcepaper

Screenshot of Figpack

Figpack

Python package for interactive scientific visualizations as self-contained HTML bundles: portable, reproducible, and suitable for long-term archiving.

homesource

Screenshot of Stan Playground

Stan Playground

Browser-based editor and runtime for Stan models: edit, compile, run, and analyze results with no local installation (with Brian Ward and Jeff Soules).

livesource

Screenshot of Isosplit

Isosplit

Non-parametric clustering with no adjustable parameters, based on Hartigan's dip statistic and isotonic regression.

source

Screenshot of LINDI

LINDI

Cloud-friendly file format and Python library for NWB data, compatible with HDF5 and Zarr and designed for linking to remote datasets (with the NWB team).

source

Screenshot of simple_ans

simple_ans

Simple, efficient lossless compression of integer datasets via Asymmetric Numeral Systems.

source

Screenshot of MCMC Monitor

MCMC Monitor

Real-time tracking and diagnostic visualization of Stan MCMC runs in the browser (with Jeff Soules).

source

Screenshot of SpikeInterface

SpikeInterface

Unified Python framework for spike sorting and electrophysiology analysis; part of the original team.

docssource

Screenshot of FINUFFT

FINUFFT

Fast, parallel library for the nonuniform fast Fourier transform on CPU and GPU; co-developed the original version with Alex Barnett.

docssource

Screenshot of Remfile

Remfile

File-like object for reading remote files over HTTP, optimized for h5py.

source

Also: the Concept Collection, a set of small proof-of-principle examples and interactive demos, many runnable directly in the browser.

Older projects

  • Figurl — shareable interactive figures; replaced by figpack
  • Kachery — content-addressed storage for sharing scientific data; replaced by figpack
  • SortingView — interactive spike-sorting visualizations; replaced by figpack
  • MountainSort 4 — replaced by MountainSort 5
  • SequenceTree — visual MRI pulse sequence programming