Open for (neuro)science tutorials: Introduction to the Allen Brain Map

Thanks for attending the webinar or viewing the video of the Open for (neuro)science: Introduction to the Allen Brain Map! This webinar provided an overview of the resources available through the Allen Brain Map, why they’re useful, and how to access them.

Please feel free to chime in here with additional questions or follow-up questions to those asked at the live webinar. You can find the recording of this webinar and information about other webinars in this series here .

Question: I’m working on neural circuits of anxiety, using optogenetics, fiber photometry and behavioral analysis. as well as immunohistochemistry. I usually get lost on which ways to use the atlas data and how to extract data for immunohistochemistry as well as stereotaxic surgeries.

Kaitlyn (live answer): I think one thing that’s going to be very useful for you is the CCF, the Common Coordinate Framework, which can help you register your data to a common coordinate space. We’re going to have a tutorial coming up that demonstrates how to use that in more detail than I have time to cover. As far as mapping our mouse atlas data to anatomy, an easy way to do that online is to go into any one ISH experiment, hit the button in the top right corner of the viewer window that looks like a box with an arrow pointing out of it, and then hit the button that looks like a key in the window that pops up showing the slices. This will put the ISH images side by side with our annotated reference atlas and the corresponding Nissl stain slice. You can also download the selected images from here showing all three views (annotation, ISH, Nissl) for later reference or to use in a manuscript or presentation.

Question: Can you show us an example of how to search for co-expression of genes alongside a selected target gene in the atlas?

Kaitlyn (live answer): In the human brain atlas, search for your gene of interest using the search box as usual. Select your gene and probe of choice from the list that pops up, using the checkbox on the left side of the list, then hit the “Find correlates” button on the far right side of the heat map. This will search by probe, so the top correlations that pop up will likely be other probes for the same gene. You can also filter the correlation search to only be within regions of interest (e.g., what genes are correlated with your gene of interest in hippocampus only?).
Kaitlyn (additional details): In the mouse brain atlas, also start by searching for your gene of interest. Like in the human search where you need to pick one gene probe to do the correlation search, in the mouse you will need to pick a coronal vs. sagittal experiment (if both are available). Select its checkbox, select whether you want to search correlations in coronal experiments only, and like in humans, you can search correlations only within a defined brain region instead of brain-wide if you want.

Question: Can Allen Institute differentiate specific IPSCs into neurons for us?

Kaitlyn (live answer): We don’t offer services to differentiate our Allen Cell Collection lines, but we do have instructions on the website on how to care for and differentiate these cells. The care instructions are listed with the ordering information.

Question: Do you collect EEG recordings?

Kaitlyn (live answer): No, we don’t currently collect any data with any living human volunteers.

Question: Can you review how to access EPhys data? And how to download?

Kaitlyn (live answer): Our older electrophysiology data can be found by going to the home for the Allen Cell Types Database (or from, click on the circle icon for the database), then selecting “Cell Feature Search.” From here you can download electrophysiology data from each cell individually, or use the “Download cell feature data” button at the top right to download for all cells. This data is also accessible via our API.
For the electrophysiology data contained in the patch-seq database, click on its icon on the home page of, and you’ll be taken to a list of download links. For more on this, see the upcoming tutorial on this dataset here.

Question: I am patching from LC interneurons in the brain stem and I just read the documentation for patch seq which seems to be very complicated. Is there any course for people getting hands-on experience for patch seq procedure?

Kaitlyn (live answer): The patch-seq data will be covered in an upcoming webinar tutorial. We don’t have plans to run a live tutorial yet. Learn more about training and tools here.