Spoiler Alert: We’re on GitHub!

The ever-enterprising Zach Sheldon set us up a GitHub today. As we are putting together papers and analyses this year, expect to see a fair amount of code going up, including the analysis for Zach and lab alum Chris Glaze’s upcoming paper on the effects of social dependent norepinephrine from Locus Coeruleus on the LMAN-RA synapse in zebra finches (currently in review).

find us at https://github.com/marcschmidtlab


Data Post

Hi there!

This week we have some images we’ve gotten after a fair amount of pain staking work (by both lab all-star and intramural Frisbee champion, Jessie Burke, and Lab Alum Collyn Messier). We’re working to close the song circuit in the female cowbird, and part of the challenge is getting the connections in the thalamic nucleus DLM (dorso-lateral division of the medial thalamus, for those keeping score at home). Here we have labeling in DLM from an injection in Area X. The video is a 3d reconstruction from a z-stack of confocal images (Thanks to Andrea Stout, PhD for helping Jessie get these images!). The blue is Hoechst stain of neurons in DLM. The red is CTB.

Stay tuned for more exciting news (and eventual publications).



Announcing Smart Box

I said I’d update this once a week, so here I am one week later. This week I have a follow up from last week’s teaser: a git repo for automating song playback while making it conditional on baseline motion. This is fairly important for some of the work we’re starting next week, but it should be broadly applicable for behavioral experiments if you want to adapt it a bit.

Shoot me (Ammon) a message if you’re interested.




April Fools, we made a post!

Hi loyal readers, I realized I have been far too focussed on moving myself towards graduation, and have allowed the website to fall by the wayside once again. Starting today, I’ll aim for weekly updates (hopefully this manages to make it to next week).

This week, we have a great option for a screen saver: motion detection of cowbirds. This is part of a larger script I’m writing to automate our playback experiments that are starting in a couple weeks. Feel free to play music in the background to improve the experience.

Announcement wise, we’re excited to welcome Marc Badger to the aviary project. He’s been here for a couple months already, and has already made a huge impact. Stay tuned for exciting (perhaps weekly) developments.


New Review on Cowbirds

This is actually old news, but our review on the possible functions of the “song system” in non singing females is out in Behavioral Processes. Check it out!

Perkes, A., White, D., Wild, M. and Schmidt, M., In Press. Female Songbirds: The unsung drivers of courtship behavior and its neural substrates. Behavioural processes.


Back to work

We’re back! The past 12 months have kept us busy, and updating the website has slipped in priorities. There’s plenty to talk about, so I’ll try to keep a somewhat close to weekly schedule.

Today, we’re happy to welcome Luke Anderson to the lab. As a new grad student, he’ll bring an additional behavioral (and perhaps field) component to our lab, so we’re all looking forward to beautiful pictures of birds doing interesting things.

Here’s a picture of Luke doing what we do best: laying the foundation for a new type of aviary.


The Cage of Dreams

We built an aviary! After years of planning, we’ve taken a bit step towards a smarter aviary. It may look like a fairly standard wire cage, but it’s actually a high-tech tool of ground-breaking neuro-ethology.

Left, sketches of our plans from 2015. Right, our newly constructed aviary.

There’s still plenty of work to do, both inside and outside. But we’ve come a long way. Stay tuned!


Website is live!

After being invisible to Google for months, our website is live. Welcome, potential visitors. With the added visibility, we’ll be making further updates to make it more useful to visitors and lab members. Check back in regularly. In the mean time, here is the most exciting 2 minutes of television you have even seen:


Grant Accepted

Our MRI grant with Kostas Daniliidis (and Dani Bassett, Erol Akcay, David White, Jianbo Shi, and others) was accepted! What started as a mad dream sketched on scratch paper is now an NSF funded project which is already well underway.

For those who don’t know, we hope to use computer vision and audio recording to track behavior in real time, allowing for large scale analysis of social behavior and online manipulation. Thanks to everyone for your continued support of this project. Read more about it here: http://nsf.gov/awardsearch/showAward?AWD_ID=1626008 


drawing by Ammon Perkes
Early drawing of the smart aviary (April 6, 2015)


Disclaimer: this was before I took a class on perspective.
“Artists” rendition of smart aviary.