Resources

Chronic Neuropixels in Mice

I developed protocols to chronically, recoverably implant single Neuropixels 1.0 probes or dual independent Neuropixels 2.0 probes into mice and record during a freely moving automated (non)match to direction task. Check out Open Neuroscience for a detailed description.

Protocols

• Full collection
• Assembly
• Implant surgery
• Explant surgery
• Building a SpikeGLX rig with camera
• Building the maze and integrating with freely moving recording

Scripts and Build Files

• Chronic implant
• Task maze and video acquisition

Parts Lists

• Neuropixels acquisition system
• Machine vision camera
• Freely moving apparatus and tracks

Publications

• code and data for Aery Jones et al, 2021
• code and data for Jones et al, 2019

DEI

I wrote 2 tools to assist with some of my own diversity & inclusion goals

1. Speaker finder: given a list of keywords, searches bioRxiv & Pubmed and returns the authors with the most publications that match that keyword
2. Citation overrepresentation tool: given a bibliography, returns which labs, institutions, & journals you cite the most

Mentorship

• How to write grad school application essays
• How to interview for grad school
• Advice to new grad students
• Workshop I developed to teach new scientists how to dissect papers
• An outline to structure mentorship of a summer intern
• My NSF Personal Statement and Research Proposal
• Using templates for lab notebooks is a great way to make sure you never forget to write anything down for your experiments. Here are the templates I use for my thesis experiments and my postdoc experiments to collect in vivo ephys data.

Teaching

• Workshop to introduce biology grad students to coding
• Seminar on mammalian adaptions to low oxygen environments at high altitudes and deep depths
• Seminar on mammalian adaptions to low water environments in deserts and at sea
• 2-hour minicourse on human evolution including a species evolution RPG activity

Course Projects

• Neuromatch Academy project: Extracting latent states from V1 spiking data
• Animation of the response of the preipheral nervous system to acetylcholine binding M2 receptors
• Evolutionary computational model of child language acquisition using a genetic algorithm based on universal grammar writeup and repository
• Literature review comparing prenatal nicotine exposure to ADHD

Course Notes

• Cell Biology (Fall 2011, Dr. Ades)
• Mammalian Physiology (Spring 2011, Dr. Higgins)
• Mammalian Physiology Lab (Fall 2012, Dr. Bierman)
• Diseases of the Nervous System (Spring 2013, Dr. Singer) and a condensed version

Other

• Unix cheetsheat
• R & ggplot cheatsheet
• Coronavirus fabric mask sewing instructions