• GraFT: Graph Filtered Time-trace analysis for decoding functional optical imaging. Works on dendrites, widefield, and somatic imaging.  github link
  • Neural Anatomy and Optical Microscopy (NAOMi) simulation code. bitbucket link. Data is available here:
  • Earth-mover’s regularized dynamic filtering (EMD-DF) code (relevant SPL paper & arxiv link) in MATLAB is currently available via this zip file.
  • SEUDO: Code and GUI to detect and correct false transients in calcium imaging data. (Currently in beta testing; for early access please email us at [email protected])
  • Code to fit flexible modulated Poisson model from the “Dethroning the fano factor” paper: GIT repository link
  • Code for source separation software (Sparse convolutional iterative shape matchine; SCISM) for stereoscopic volumetric imaging: GIT repository link
  • Statistical Dictionary Learning Library:,
  • Dynamic Filtering for Sparse Signals: .zip
  • Spatial Filtering for Sparse Signals: .zip
  • LaTeX equation image maker for Linux (BASH shell script): latexit_bpp. Place in searched folder and use $latexit_bpp -h for help (or look in the comments).


  • Information on Parallel Computing with MATLAB: pdf
  • Derivation of the Kalman Filter using a Bayesian approach: pdf

Presentation Slides

  • Causal LCA presentation given at the 2011 DSP Workshop in Sedona, AZ (Presented at the best student paper competition): pdf
  • Sparse Dynamics Presentation given at the 2011 CISS Conference on March 23rd, 2011 in Baltimore, MD: pdf
  • Hierarchical approach to Sparse Dynamics. Presentation given at the SPARS11 Conference on June 28th, 2011 in Edinburgh, Scotland, UK: pdf