Coding Tutorials

Coding Modules:

Connectome Annotation Versioning Engine (CAVE) a computational infrastructure developed to manage, proofread, and analyze large connetomic datasets efficiently and collaboratively

The MICrONS dataset, spanning one cubic millimeter of mouse cortex, is comprised of petabytes of data from electron microscopy images at nanometer resolution, dense segmentation of 200,000 brain cells, half a billion synapses, and hundreds of thousands of other annotations to label the data.

To enable systematic analysis without downloading hundreds of gigabytes of data, users can selectively access cloud-based data programmatically through a collection of open source Python clients.

This collection of Ipython Notebooks introduces data access to the Connectome Annotation Versioning Engin (CAVE).

Introduction to MICrONS

These notebooks introduce core concepts of analysis for connectivity, cell typing, and morphology.There are two options

Cloud Access with Google Colab This is will run in the browser. Go to File > Save to Drive to keep a working copy.

Local setup notebook Ipython Notebook This is a notebook rendered to the broswer in .html. will run in the browser. Download the notebook from the link in the right menu.

(Optional) Setting up persistent data access

These notebooks are foundational for accessing the data, but only need to be completed once per user. There are two options:

• Cloud Access, for setting up access in Google Colab
• Local Analysis setting up access for running on a local machine or JupyterHub. We recommend Cloud Access for intitial instruction and in-class work. Local analysis may be better for independent study and ongoing work.

Cloud Access with Google Colab This is will run in the browser. Go to File > Save to Drive to keep a working copy.

Local setup notebook Ipython Notebook This is a notebook rendered to the broswer in .html. will run in the browser. Download the notebook from the link in the right menu.