The Hemibrain dataset, released in January 2020, was managed by DVID for most of its production. We are providing a replica of our production DVID system and the databases, complete save for some irrelevant data for outside use.
The grayscale image volume
The grayscale data is available through your own local DVID server (165 MB) with data storage provided by a Google-owned cloud storage. Just follow the README instructions after unpacking the downloaded tarball.
All other reconstruction data
While the above grayscale server uses data in the cloud, our production DVID server for reconstruction requires a reasonably powerful server (depending on the anticipated user load) and a slightly more involved installation process. First, you'll have to download the DVID system (identical to the above grayscale download save a different TOML configuration file). Then, you'll have to download databases to local disks before starting the server.
Step 1: Download the DVID system
First, download the DVID packaged tarball file (168 MB, preconfigured for this dataset) and untar it:
% tar xjvf hemibrain-dvid.tar.bz2
If you download through the browser, it's possible it will automatically uncompress the file and
you'll already have a
tar file without the
bz2 extension. When untarring the file, you may
Ignoring unknown extended header keyword errors if you are on Ubuntu. That's OK and is just extra
Mac tar file data that can be ignored.
Within the untarred directory
hemibrain-dvid is a configuration file
hemibrain-release.toml. This configuration assumes you are
downloading the databases to a sibling directory
the following directory structure:
/mydir/databases/hemibrain-dvid (directory containing the untarred dvid release)hemibrain-dvid.tar.bz2
If you choose to store the databases at different locations, edit
hemibrain-release.toml to point to the appropriate directories. This
will also allow you to distribute the databases to different disk drives.
We recommend using NVMe SSD drives
due to their exceptional performance.
If you are also running a grayscale dvid server, you must change the ports on either that one or this dvid server since both are by default using ports 8000 and 8001. For example, change the grayscale dvid server TOML file to use ports 9000 and 9001 then restart that server. You will then be able to access the grayscale image volume on port 9000 and all the other reconstruction data on port 8000.
Step 2: Download the databases that you need
Our original databases have data at 50+ timepoints, but for this release, we've reduced the data to three versions: one of the earliest versions in 2018, an intermediate version after revising the synapses, and the final version published as part of our Hemibrain release. This brings down the size of the databases to 1.2 TB. You can choose which of the databases you'd like to download (segmentation, other labelmaps, synapses, meshes, etc). If you choose not to download a database, the data from that database won't be available but the DVID system will still work.
The databases are available in the following Google Cloud Storage bucket: gs://hemibrain-dvid-segmentation/databases
We suggest using the Google gsutil tool: https://cloud.google.com/storage/docs/gsutil
databases directory that is a sibling of the untarred DVID package,
then download the databases you want. The following commands assume you are in
the directory you downloaded the DVID packaged tarball file.
% mkdir databases # should be sibling of the untarred hemibrain-dvid directory% gsutil -m cp -r gs://hemibrain-dvid-segmentation/databases/metadata databases% gsutil -m cp -r gs://hemibrain-dvid-segmentation/databases/segmentation databases% gsutil -m cp -r gs://hemibrain-dvid-segmentation/databases/mutlog databases...% chown -R me:mygroup databases # makes sure you can actually write to those DBs
You are required to download the small "metadata" database but can choose some combination of the other databases. The full dataset is comprised of the following databases:
|718 GB||segmentation||Highly compressed supervoxel |
|3.5 GB||mutlog||Required if using segmentation. Supplies the supervoxel-to-label mappings|
|225 GB||other-labelmaps||Mitochondria, ROIs, etc.|
|145 GB||meshes||Neuroglancer format|
|47 GB||synapses||Pre- and post-synaptic annotations|
|10 GB||keyvalues||Similar to a versioned file system with JSON files, etc|
|38 GB||annotations||3d point annotations like bookmarks|
|1.7 GB||rois||Regions of Interest|
Step 3: Run the server
From within the
hemibrain-dvid directory, launch dvid using the appropriate
executable for your platform.
1) For Linux:
% linux/bin/dvid serve hemibrain-release.toml
2) For Mac
% mac/bin/dvid serve hemibrain-release.toml
If you are running macOS Cataline (10.15) or newer, Apple has increased software protections that can lead to your being unable to run the program.
In order to workaround the problem, please execute the following
% xattr -r -d com.apple.quarantine mac/lib mac/bin
If you are successful, the server will log messages to /tmp/hemibrain-release.log or whatever directory is specified for logging in the hemibrain-release.toml file in this directory. You can modify that TOML file to configure your server including the ports it runs on. You can use the browser to inspect the dvid server using http://localhost:8000.
Other useful commands to try:
% tail -f /tmp/hemibrain-release.log% <os>/bin/dvid about% <os>/bin/dvid help