Data Access

Data hosted by neurodata.io are publicly available. NeuroData utilizes the BOSS, co-developed with JHU-APL, as a data store. This document explains how to access this data.

BOSS has the following hierarchical organization:

  1. Collection: typically either the name of the lab PI or the person who collected the data

  2. Experiment: within this level, data share a common voxel extent and voxel size. Often synonymous with actual experiments.

  3. Channel: data reside at this level and are either uint8/uint16 image data or uint64 annotations

Methods for accessing data

All data access currently requires registration. Create an account at api.boss.neurodata.io

ndwebtools

A frontend for navigating BOSS projects. It provides (limited) TIFF cutouts to data and links to data visualization. Larger cutouts (> 1GB) should be performed programmatically using one of the tools 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 the channels within the experiment.

ndpull

A Python package for downloading volumes of data from the BOSS as TIFF stacks. This tool is installed locally and used from the command line.

  • Installation and usage instructions on its GitHub page

intern

A Python package developed by JHU-APL for interactively and programatic usage of the BOSS.

  • Installation and usage instructions available on its GitHub page

Questions/comments? Email support@neurodata.io