Our own designs and code

Our GitHub page has links to some hardware and software projects from our lab:

We use and strongly endorse the following:

Linux Mint, Anaconda Python, The R Project, GNU Octave, LibreOffice*, Inkscape**, GIMP

* – Mark switched from MS Windoze and Office when the lab was launched a LONG time ago and has used LibreOffice for hundreds of grant proposals, manuscripts, and other docs. Give LibreOffice a go. Its easy to use and has all that any scientist needs to be productive with documents.

** – Inkscape is free alternative to Illustrator; much improved in recent years; has everything needed to produce production ready graphics for scientific presentations and manuscripts; the Deep Ungroup addon is so handy

Other stuff


  • Arduino – An amazing microcontroller that has so many uses in our lab.
  • Teensy – A bit more advanced compared to Arduino, and an emerging key tool for our lab
  • OpenMV – A microPython based microcontroller with integrated  camera; on its way to becoming the video recording and behavioral control system for our lab’s future
  • The Imaging Source – GigE cameras

Software (Python)

  • jupyter (mothership; why Mark was able to break his Matlab addiction)
  • numpy (crucial numeric library for Python)
  • pandas (crucial library for data frames and easy interchangeability with R)
  • matplotlib (fantastic graphics library)
  • seaborn (graphics library that makes life so good)
  • rpy2 (memory space link to R)
  • oct2py (memory space link to GNU Octave)
  • EEGLab (time-locked cross-trial time-frequency analysis (LFP etc); written for Matlab and works just fine with GUI under GNU Octave)
  • neurospec (coherence analysis (e.g. spike-field); written for Matlab and works just fine with GUI under GNU Octave)

Select vendors

  • Adafruit – electronic parts and custom designs
  • A-M Systems – wire and other supplies for ephys
  • Braintree – all kinds of lab gear
  • Microprobes – microwire arrays, optrodes, pharmatrodes
  • MedAssociates – behavioral system (MedPC) and parts
  • Neuroexplorer – software for ephys
  • OpenEphys – open source hardware for ephys
  • Plexon – hardware for ephys; used by our PI since the beginning of time
  • Prizmatix – high power LEDs and other gear for opto and photometry
  • Plastics One – cannula for drug infusions
  • pyPhotometry – Open source, Python based, fiber photometry
  • Sparkfun– electronic parts and custom designs
  • Stoelting – all kinds of lab gear
  • ThorLabs – optics stuff; lab snacks!
  • Tocris – our primary vendor for research grade drugs and other pharma
  • Tritech Research – off-label microscopes and surgery gear
  • WPI – wire and other supplies for ephys