What is the discussion?
Lex Kravitz and Mark Laubach will host the Hack Chat on Wednesday, February 19, 2020 at noon Pacific Time. Time zones got you down? Here's a handy time converter! Unless, of course, you look inward to the most wonderfully complex structure ever found: the brain.
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Open source tools and neuroscience, and the OpenBehavior project
Can everyone introduce themselves please
Sure, are we good to get started? I'll kick off with a bit of an intro: My name is Lex Kravitz and I am a professor in the Psychiatry department at Washington University in St Louis. With our co-host, Mark Laubach, we started a website, Openbehavior.org, in 2016, to further open-source methods in behavioral research. In the intervening years, it seems that many people in the scientific community have started using and publishing open-source methods, so we’re here to share a few interesting projects with this community, and also answer any questions about neuroscience, research, life, etc!
Im A Essa (discontinued Phd in AI) and software engineering bsc
I'm Mark Laubach. I am a neurobiologist, with lab at American University in DC. We study how decisions are made in the brain, and use a lot of custom made tech in our research.
Yes, please, let's start. And welcome Mark and Lex!
Thanks! I thought we'd start by sharing our website and highlight some of the more interesting projects that we've covered on it
Camera Control is an open-source software package written by postdoctoral fellow Gary Kane that allows video to be recorded in sync with behavior. The python GUI and scripts allows investigators to record from multiple imaging source camera feeds with associated timestamps for each frame.
Read this on OpenBehavior
We made a website, openbehavior.org, with the goal of promoting open-source methods in neuroscience. It's something Mark and I do for fun, along with the students in his lab, mainly Sam White and Linda Amarante. Maybe we can start with some youtube videos to demo some cool recent advances in open source neuroscience?
One of my favorite open-source tools (that has been hugely influential in behavioral neuroscience over the last year) is DeepLabCut:
This is a markerless pose-tracking package, that has been used to improve video tracking of mice, flies, and *many* other laboratory applications
That's pretty cool
Wow, that's exactly what I tried to design in my old job 20+ years ago! We wanted to track where a rat was pointing his nose. Machine vision just wasn't up to the task at the time
@Dan Maloney That was my Master's project in 1990! Did not work so well.
Cool! yeah most methods before this used "markers" - a piece of tape or something like that
Perhaps you can define the difference between random movement, purposeful movement and a behavior?
how did you solve that? training etc?
Intro for me (Charlie L aka CyberchuckTX)
: lifelong geek/nerd/programmer interested in these topics.
BTW, "openbehavior.org" times out when I try to access it ...
Beyond being an amazing application,...
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