StereotaXYZ — pronounced "stereo-tack-seas" — aids in the empirical design and per-animal customization of stereotactically targeted procedures. This is particularly relevant when performing interventions at odd angles through high skull shape variability areas (e.g. the occipital or nasal bone plates) or areas which are difficult to access e.g. due to the proximity of tough or vital tissue.
In addition to implant design functionality, StereotaXYZ ships with a plotting utility, which allows visual inspection of implant designs with.
- MRI-Guided Targeting of Deep Brain Circuits: StereotaXYZ, at the 2018 Swiss Society for Neuroscience Annual Meeting in Zurich (CH).
The following examples assume that in addition to an installation for StereotaXYZ, the example data from our repository is also available on your machine. You can make it available under the expected path of the examples, as follows:
cd
mkdir src
cd src
git clone https://github.com/IBT-FMI/StereotaXYZ.git
StereotaXYZ can produce volumetric data representations of all elements of interest, registered to the coordinate space of a template. Angles can be specified in 3D - meaning that the elements of interest are not constrained to a specific YZ or XZ plane. In this case, YZ and XZ angles have to be unambiguously specified.
This full 3D-aware visualization can be obtained from the stereotaxyz plot3d command line interface (internally calling the stereotaxyz.plotting.xyz() function).
A basic usage example of this function is:
stereotaxyz plot3d ~/src/StereotaXYZ/example_data/skull_6469.csv DR -p 45 --reference "bregma skull" --save-as 6469_3d.png
Which produces the following image (incidentally, all elements here lie in the same YZ-plane, but this is not required):
A simple 2D visualization of the elements of interest can be created with the stereotaxyz plot2d command line interface (internally calling the stereotaxyz.plotting.yz() function).
A basic usage example of this function is :
stereotaxyz plot2d ~/src/StereotaXYZ/example_data/skull_6465.csv DR -p 45 --save-as 6465_2d.png
Which produces the following image (here, all elements are required to lie in the same YZ-plane):
In case no visualization is needed, the computed coordinates for reaching a defined target at a defined angle can be outputted as text.
This is done via the stereotaxyz text command line interface.
A basic usage example of this function is:
stereotaxyz text ~/src/StereotaXYZ/example_data/skull_6469.csv DR -p 45 --reference "lambda skull"
Which returns the following text to the terminal:
You have selected:
Target: "DR"
LeftRight(lambda skull): 0.00
PosteroAnterior(lambda skull): -0.60
InferoSuperior(lambda skull): -3.40
Entry Angles:
XZ(yaw, from Posteroanterior axis): 0°
YZ(pitch, from Posteroanterior axis): 45°
Given your skull points, you can best reach the target at the desired angle with:
Icision Site:
LeftRight(lambda skull): 0.00
PosteroAnterior(lambda skull): -3.15
InferoSuperior(lambda skull): -0.85
Insertion Length: 3.61mm
##Getting Started
To use the software, after installing it, you will need to:
- Create a “Skullsweep” file analogous to the example file distributed with the software.
- Choose a reference point (most commonly bregma) for all your measurements; lambda can also be used as a reference, but if you use it, be sure to specify lambda's cordinates relative to bregma (as we do in the example file).
- Fill in skullsweep point coordinates (best recorded by lowering a thin pipette or stylus until it makes contact with a properly restrained and positioned animal's skull).
- Enter the coordinates for any targets you might want to reach; these are best extracted from an atlas or a preliminary MRI recording of the animal.
- Run any of our command line interfaces, specifying the desired target and the desired angle of entry.
StereotaXYZ is distributed with a .gentoo specification installation instruction. If using a Gentoo system, you can simply clone this overlay, and use the associated script to install the software, and automatically handle all of its dependencies. As root, run:
git clone git@github.com:IBT-FMI/StereotaXYZ.git
cd StereotaXYZ/.gentoo
./install.sh
Non-live versons of this package will be available for Gentoo via the Science Overlay as they are released.
Python's setuptools allows you to install Python packages independently of your distribution (or operating system, even).
This approach cannot manage any of our numerous non-Python dependencies (by design) and at the moment will not even manage Python dependencies;
as such, given any other alternative, we do not recommend this approach:
git clone git@github.com:IBT-FMI/StereotaXYZ.git
cd StereotaXYZ
python setup.py install --user
If you are getting a Permission denied (publickey) error upon trying to clone, you can either:
- Add an SSH key to your GitHub account.
- Pull via the HTTPS link
git clone https://github.com/IBT-FMI/StereotaXYZ.git.
Python's setuptools allows you to install Python packages independently of your distribution (or operating system, even);
it also allows you to install a "live" version of the package - dynamically linking back to the source code.
This permits you to test code (with real module functionality) as you develop it.
This method is sub-par for dependency management (see above notice), but - as a developer - you should be able to manually ensure that your package manager provides the needed packages.
git clone git@github.com:IBT-FMI/StereotaXYZ.git
cd StereotaXYZ
echo "export PATH=\$HOME/.local/bin/:\$PATH" >> ~/.bashrc
source ~/.bashrc
python setup.py develop --user
If you are getting a Permission denied (publickey) error upon trying to clone, you can either:
- Add an SSH key to your GitHub account.
- Pull via the HTTPS link
git clone https://github.com/IBT-FMI/StereotaXYZ.git.
To install the software you will need to have the following packages available on your system.
This is handled automatically if you install the software via a package manager (e.g. Gentoo's Portage) - if not, you will have to ensure that these packages are available manually.
If you try to run the software without having the dependencies on your system, you will get ImportErrors letting you know which package is missing.