CAVE for Users

There are many ways to approach using connectomics data. Sometimes you need to explore volumes and interact directly with the data, while other times you want to examine quantiative analysis or build programmatic pipelines. CAVE was designed to be used in diverse ways through a collection of different tools.

Documentation for users

Broadly speaking, we have split documentation into two categories of user interaction:

Interactive Data Exploration. How do you navigate a dataset online in tools like Neuroglancer? What can you see and do as you look at large, segmented 3d image volumes?

Programmatic Data Analysis. How can you download and process connectomic data at scale? How do you download meshes or query synaptic connectivity?

Public CAVE Datasets

The best way to see how CAVE works is to see it in action. A number of datasets using CAVE are publicly available and can be used for analysis and exploration. In many cases, these datasets have their own rich documentation that can suggest how to use CAVE tools for your needs.

MICrONs Visual Cortex (Mouse)

The MICrONs dataset1 covers approximately a cubic millimeter of mouse visual cortex across all layers with millions of proofreading edits. A collection of tutorials describe not only the dataset, but also setting up CAVEclient, exploring the data, querying CAVE annotatoin tables, and accessing meshes and skeletons of neurons and other structures.

FlyWire (Fly brain)

FlyWire2 used CAVE to manage and proofread a complete reconstruction of an adult Drosophila brain. In addition to tutorials for using CAVE to query and analyze fly connectome data, FlyWire also provides a “sandbox” view of EM segmentation to experience proofreading in Neuroglancer. To use the sandbox, go here, register, and then use the dataset menu in the top right corner to change from public release, a static view of the data, to “Sandbox”, an editable view of the data.

FANC (Female Adult Nerve Cord)

The FANC project3 reconstructed a ventral nerve cord of an adult Drosophila to learn about somatosensory and motor organization. The project documentation offers examples of interactive and programmatic analysis of the data.

H01 (Human cortex)

The H01 dataset4 is reconstucting a portion of adult human cortex. Proofreading in CAVE is ongoing, and their project documentation nicely describes the proofreading process and even offers a sandbox to try edits.

Footnotes

  1. Allen Institute for Brain Science, Seung lab at Princeton University, and Tolias lab at Baylor College of Medicine.↩︎

  2. Seung and Murthy labs at Princeton University↩︎

  3. Lee lab at Harvard University and Tuthill lab at University of Washington, Seattle↩︎

  4. Lichtman lab at Harvard University and Google Connectomics↩︎