Software:

• Calcium imaging analysis
  • Suite2p - Registration and source extraction.
  • MLSpike - Event detection algorithm that works well for extracting climbing fiber events in Purkinje cell dendrites. Used in our 2019 and 2025 papers.
• Electrophysiology analysis
  • Kilosort 4 - Semi-automated spike sorter. You can also use this through SpikeInterface.
  • Phy - Our preferred software for manual curation of spike sorted data.
  • Bombcell - A resource for semi-automated curation of spike-sorted data. Used to get clean ground-truth units in Beau et al., 2025.
  • Awesome Neuropixels - a compiled set of resources for state-of-the-art use of Neuropixels probes.
  • NeuroPyxels - Friend of the lab Maxime Beau’s analysis package that has lots of helpful functions for analyzing and plotting data in Python. Designed for Neuropixels electrophysiology data but useful for all kinds of analysis.
• General data analysis
  • dkNeuroLab Github page - where you can find code associated with our papers.
  • GLMnet - Generalized Linear Model fitting software, See Jonathan Pillow’s tutorial at the 2018 Cosyne meeting for a very useful primer.

Hardware:

• Microscopes - We have worked extensively with Dale Elgar at Cosys.
• We try to build as much of our equipment as possible in-house. Stay tuned for an detailed description of our behavioural setups.

Textbooks:

• Spikes - a surprisingly accessible computational neuroscience textbook.
• Foundations of Cellular Neurophysiology - the best cellular neurophysiology book. Very useful for grounding your systems neuroscience understanding in biophysics.
• The Cerebellum as a Neuronal Machine - a classic piece of text.

Primary literature, essays, and reviews that quantify inequality:

• Indira Raman: Power analysis
• Dworkin et al., 2020, The extent and drivers of gender imbalance in neuroscience reference lists - It’s probably worse than you think.
• Racial disparities in funding rates in the US at the NIH and NSF. Data from 2021-22.
• The UK’s demographics stats for academia 2024/25 - yikes.

Links and resources:

• BiasWatchNeuro’s lists of diverse speakers
• The SAFE Handbook - a tool for improving lab culture