Description of DAPI template
This repository contains a three-dimensional population-based average atlas, the DAPI template, of the C57BL/6 mouse brain stained with the commonly employed fluorescence nuclear stain DAPI. The DAPI template, accompanying segmentation, and a simplified segmentation can be found as nifti files in data/. Moreover, the repository contains all the raw data (data/mice/) and the full code base (template_creation_pipieline/) which was used in the construction of the teamplate.
The DAPI template, is constructued from consecutive coronal brain slices of 12 male mice aged between 10-11 weeks. Each mouse brain is first reconstructed into a three-dimensional volume and then an iterative averaging process of these reconstructed brain volumes was employed to yield the final population-based average.
The repository also includes an automatic segmentation/spatial normalization pipeline (automatic_segmentation_program/) for novel coronal slices described below.
Automatic slice segmentation
Program for automatic segmentation to a DAPI-stained coronal mouse brain slices.
Getting started
- Setup your environment with the correct python version, python packages, and Advanced Normalization Tools (ANTs).
- Download the and unzip the example folder.
- In a terminal window, navigate into the unzipped example folder.
- Run the runner_example.sh with the command
bash runner_example.sh
- The automatically created segmentation can be found in
Brain_example/Segmentation.nii
For detailed parameter and output description go to the automatic segmentation program.
How to setup the environment
Below is a quick guide to setup the enviroment on a UNIX (Mac and Linux) system
To check the version of a package
pip freeze | grep nibabel
Install ANTs, preferably using precompiled binaries, available (for Mac/Linux) at
https://github.com/ANTsX/ANTs/releases/tag/v2.1.0
Create ANTSPATH and add it to your path. This is done by editing the config file for the terminal shell. The config-file is often named
~/.bashrc
or
~/.bash_profile
In the config-file add the following lines
export ANTSPATH=usr/local/bin/ANTs
export PATH=$PATH:$ANTSPATH
Here, ANTs was installed in /usr/local/bin/ANTs
After adding this to the config-file, restart the terminal and test if the
path was added correctly by typing
which antsRegistration
The correct path should then be printed.
- if permission is denied, the file needs to be made executable - this is done using the command
sh
chmod +x <...>/antsRegistration
## Prerequisites
* A high-resolution, DAPI modality TIFF image of a coronal mouse brain slice. Can have multiple channels.
* The DAPI template file (.nii or .nii.gz)
* A segmentation of the DAPI template (.nii or .nii.gz)
## Usage
Use runner.py to preprocess and output a segmentation registred to the slice. For detailed parameter and output description go to the automatic segmentation program.
