How to download Allen Connectivity Atlas and perform EDA (Exploratory Data Analysis)?

I am very new in this area and want to download Allen Mouse Connectivity Atlas and perform EDA (Exploratory Data Analysis) on it. Then visualize principal components of the 3D image dataset. All in python. Any guidance? I used this link" Mouse Connectivity — Allen SDK dev documentation", and after setting up the python code could download 11_wks_coronal_644250774_25um_projection_density.nrrd and when run the following code only get header data and metadata but not sure what is 3D image dataset to visualise its PCA. How can I get all the data?

I was wondering to know if you also have any slack channel to communicate easily?


import nrrd
import numpy as np

file_name= ‘C:/Users/Downloads/11_wks_coronal_644250774_25um_projection_density.nrrd’
data_array, metadata =

Hello Jin,

It sounds like you are embarking on a very ambitious project. The first step that you will want to do is to gain familiarity with the Allen Mouse Connectivity Atlas resources. The interactive web site will allow you to explore the data and do many interesting queries. The documentation will acquaint you with the experiments and data processing. See especially the “Overview”, “Informatics Data Processing” and “Mouse CCF, Reference Atlas, Version3 (2017)” documents.

Finally, the API documentation is where you can learn about programmatic resources to help you build your programs to access and analyze the data.