Using the brain observatory in the classroom


Hello everyone! Here at the UW we’ve been using the Brain Observatory in our computational neuroscience courses – as a final workshop / lecture and transition to (somewhat amazingly, I always think) actual open questions in neural coding. Students have been pretty fired up. In our intro / undergrad course, basically the students do some of the (Allen) tutorials python over the preceding week, and then a final “live” 2-3 hour workshop on putting these to work in an ipython notebook in class (and HW to explore other cell(s)). Allen colleagues helped us do everything I’ll gratefully “admit” as well as some awesome in-class teaching. Have others thought about this type of thing? Happy to share more on what we’ve tried, and what could be done better / more extensively too …



hey Eric,
I have just started doing something similar for my lab here in Zurich but on a small scale. I’m taking them through these python tutorials and answering their queries. I’d be happy to share my experience as the time progresses!

1 Like


This is fantastic! Please let us know if there’s anything we can do to support your efforts. If the materials are open, feel free to share them here. Also happy to setup an “Education” category to facilitate sharing your experiences with the broader community.

1 Like


Hi @asim and @Eric – I’m super excited to hear others are doing this as well! I’m designing a neurobiology lab course here at UCSD, the last portion of which will be a project with the Allen database. I’m also working with Brad Voytek to expand this into an entire course that will be cross-listed in our new data science program.

I’m a full time teaching professor, and was planning on developing a (hopefully comprehensive!) suite of resources (e.g. tutorials, python notebooks, etc) for teachers and students to use in order to implement these. I’m also planning on conducting educational research with them in my class, and it would be absolutely tremendous to partner up with a few other places. I’m mostly curious about how working with “real” big datasets like this one changes students’ perception of neuroscience and their place in the field.

I would absolutely love to hear what you’ve tried and talk about how we could collaborate on developing these resources!

(Also, hey @Eric, you probably don’t remember me but we met at the Dynamic Brain course several years ago!)



I’m all in favor of an education category. :slight_smile:






If I can get two more votes for an “education” category, I’ll start one.



+1 for an education category!

1 Like



1 Like



1 Like


@ajuavinett, @asim, @Eric - I’d love to hear about how you’ve developed your resources and what’s worked in your classrooms. One of the many hats I wear here is supporting educational uses of our resources just like yours! Also, if your resources are open source/access and you’re interested, we might be able to share them on our website at some point in the future. If you’d like to chat in more depth please comment and we’ll connect over email.



There is a publication from 2018 that includes hints on lesson plan creation from the Allen Brain Atlas datasets: The Allen Brain Atlas as a Resource for Teaching Undergraduate Neuroscience
There is particular detail on the in situ hybridization datasets, and use of the reference atlases.