We have imaged a full adult female fly brain at 4x4x40 nm resolution (see Zheng, Lauritzen et al., 2018). The whole brain dataset is able to be downloaded here preconfigured with a CATMAID instance so you can get started tracing. Instructions for tracing are available at the main CATMAID site here.
The dataset version here, is an alignment that improves in most places upon that present in Zheng, Lauritzen et al. (2018). In the interests of open data however, we also provide the Zheng, Lauritzen et al. (2018) alignment, instructions for how the installation differs are present at the bottom.
You will need at least 12 TB of storage space for the data and recommend Ubuntu is used. Instructions on how to set up a known system that it works on are below the general installation instructions below.
We are a small team and can't provide much individual tech support. But below we have a hardware configuration known to work. Some help may be available by emailing .
A fly through of the paper alignment is shown below
Installation can be done very simply by cloning the git repo and then running the installation scripts, however, this assumes the docker-compose system is already installed (see below under hardware)
The simplest installation method after docker has been installed as per above is to clone the repo.
git clone https://www.github.com/bocklab/temca2-catmaid
This will create a folder called
temca2-catmaid in whatever directory you were in.
From within the
temca2-catmaid/download directory, we can run the download script. On Ubuntu this is done through first installing the required libraries
pip3 install requests progressbar2
python3 download_sections.py --datapath /TEMCA2_RAID/v14_align_tps
This will then proceed to download the sections sequentially. This is a large download (~12 TB) and will take a long time. For more details see the README.md in the download directory.
To set up the CATMAID docker we should move back to the main github directory (or open a new terminal, since the previous download will take awhile) and download the top levels (for faster access) and the database file with some initial tracing
cd temca2-catmaid ./catmaid_in_a_box_install.sh
After this has run it should be initalised.
This will then make the CATMAID instance accessible from http://localhost:8000
A default user with tracing privileges is availabe under the username/password of temca2/temca2. New users can be created through http://localhost:8000/admin after logging in with the admin account (admin/admin).
For simplicity, we recommend a few pieces such as an external RAID for hosting the image stack, feel free to change upon this, but note that some configuration would be needed.
The base docker image assumes a standard 16.04 Ubuntu system. This doesn't have to be overly powerful. We have used a Dell Precision 5720 with 16 GB of RAM, i5-7600 processor and Ubuntu 16.04 pre-installed.
The following commands should then be run to ensure the software is up to date.
sudo apt-get update
sudo apt-get upgrade
The instructions for docker compose install should then be followed from here.
The image pyramid is approximately 12 TB in total size. We recommend (and the instructions assume that) these are placed in a RAID-5 setup. We have used a Mobius™ 5-Bay FireWire 800 enclosure, and five Seagate ST4000NM0035 4 TB HDDs available, for example here, and found acceptable performance.
Once the drives have been set up in a RAID-5 system (as per the manual) they should be formatted and setup to allow easy mounting in the future. As a first step, the disk location will be needed. This can be determined by running the following
lsblk --output NAME,LABEL,UUID,MOUNTPOINT,SIZE
This will give an output along the lines of:
NAME LABEL UUID MOUNTPOINT SIZE sda 465.8G ├─sda1 ESP CA75-A471 /boot/efi 600M ├─sda2 OS D88D-F5C7 3G ├─sda3 UBUNTU 8cec81af-9187-4e4c-9e71-1efbf75053b7 / 430.5G └─sda4 da65590e-d2ce-42ad-9422-04697f272ed5 [SWAP] 31.7G sdb 14.6T
You will want to look for a drive which has no LABEL, and a size of 14.6T. Assuming this is located at
sdb these can be formatted as following (NB: double check this location and change as appropriate, if it is listed as sdc change all sdb to sdc)
sudo parted -a optimal /dev/sdb mklabel gpt sudo parted -a optimal /dev/sdb -- mkpart primary ext4 1 -1 sudo mkfs.ext4 -b 4096 -i 65536 -L TEMCA2_RAID /dev/sdb1 -m 0
The directory these drives will be mounted to should then be set up and fstab modified.
sudo mkdir /TEMCA2_RAID sudo mount -L TEMCA2_RAID /TEMCA2_RAID sudo chown -R $USER:$USER /TEMCA2_RAID
In order to mount these drives upon reboot, the /etc/fstab file should be modified. This should be done using the unique device ID to this file
UUID=$(lsblk /dev/disk/by-label/TEMCA2_RAID --output UUID | sed -n 2p) echo "UUID=$UUID /TEMCA2_RAID ext4 rw,noatime,data=writeback 0 0" | sudo tee -a /etc/fstab
The base level directory should be created. Assuming you are downloading the recommended v14 alignment
The image alignment used in the paper, FAFB v13, is no longer available for download. The original v13 tracing (with low resolution imagery) remain available for replication of numerical results in the paper, but should not be used for future tracing.