Hello,
I’m using the atlas and the NeuroInfo software to detect certain cells in brain slides. At the end of the process I’m supposed to get the cell number for each region from each brain (and their coordinates), and I was wondering if there’s a better way to analyse this other than just adding them up for each region - meaning, I’d love to know how you will analyse such data (I believe you have far more experience than me in analysing cell detection) 
Thank you!
Hi @Shiri
Most of the analysis for Allen Institute projects is based on computing values in each fine structure, allowing us to “roll up” signal values in small structures. Then we can analyze at the level of the level of the Dentate Gyrus, AND at the level of the Hippocampus, for example.
Most of our projects detect some kind of signal rather than absolute cell values, so most of our analyses include a concept of both intensity and density of the signal. You can read more about this in the informatics documentation for each project. Here are the links to the docs for the Mouse Brain Atlas and the Connectivity Atlas. Each has a section about “gridding” and “unionizing” that is done to enable analysis of the signal.
Amazing, thank you!