This page explains how to access/download data hosted by NeuroData. Data are publicly available. We host our data on an AWS Open Data Bucket in Neuroglancer Precomputed format.

Data listing

The open data bucket name is open-neurodata.

With an AWS account and the AWS Command Line Interface, one can list the projects using this command:

aws s3 ls open-neurodata

Perform a cutout

To load a cutout into an ipython or jupyter session, we suggest CloudVolume, a python interface to Neuroglancer precomputed.

pip install numpy cloud-volume and run the following code:

# pip install numpy tifffile cloud-volume
from cloudvolume import CloudVolume

vol = CloudVolume(
    "s3://open-neurodata/bock11/image", mip=0, use_https=True
)

# load data into numpy array
cutout = vol[65024:65536, 62464:62976, 3616:3632]

Save cutout to TIFF

# pip install tifffile
import tifffile

# save cutout as TIFF
tifffile.imwrite("data.tiff", data=np.transpose(cutout))

neuroglancer

To visualize the data before downloading you can use neuroglancer. Links to each dataset can be found on each project's listing on OCP. Additional information on Neuroglancer can be found here.

Questions/comments?

Email support@neurodata.io