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 template.
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.
Program for automatic segmentation to a DAPI-stained coronal mouse brain slices.
Getting started
bash runner_example.sh
Brain_example/Segmentation.nii
.Brain_example/im_c2.nii
as main image and open the segmentation image Brain_example/Segmentation.nii
as segmentation. Can for instance be done in ITK-SNAP.For detailed parameter and output description go to the automatic segmentation program.
Below is a quick guide to setup the enviroment on a UNIX (Mac and Linux) system
python --version
requirements.txt
. All packages can be installed/updated using pip
. To install a package, e.g. nibabel: pip install nibabel
. To check the version of a package pip freeze | grep nibabel
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 ~/.bashprofile
. 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 chmod +x <...>/antsRegistration
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.