This document explains how to access/download data hosted by NeuroData. Data are publicly available. NeuroData utilizes the BOSS, co-developed with JHU-APL, as a data store. We also selectively host small datasets on S3 for fast data visualization in neuroglancer. For that, see our guide on the precomputed format.
- Collection: typically either the name of the lab PI or the person who collected the data
- Experiment: within this level, data share a common voxel extent and voxel size. Often synonymous with actual experiments.
- Channel: data reside at this level and are either
uint16image data or
Further information on BOSS organization can be found in the docs.
Methods for accessing data
Data access requires a free account. Create an account at api.boss.neurodata.io. All methods require a login.
There are four methods for getting data from the BOSS:
A frontend for navigating BOSS projects. It provides TIFF cutouts (limited to < 1GB) to data and links to data visualization (through neuroglancer). Larger cutouts should be performed programmatically using either
intern detailed below.
- Log in at ndwebtools.neurodata.io
- Navigate the available projects by clicking the links to collections and experiments. Clicking on any experiment takes you to the cutout page.
- The cutout page provides TIFF downloads and viz links for channels within each experiment.
NeuroData operates a fork of neuroglancer with BOSS support and color customization. The most straightforward way to load data into neuroglancer is through ndwebtools (above).
A Python command-line tool for downloading volumes of data from the BOSS as TIFF stacks. This library can also be loaded from within Python.
Installation and usage instructions on its GitHub page
A Python package developed by JHU-APL for interactive and programmatic usage of the BOSS.
Installation and usage instructions available on its GitHub page