B6_dapi_template/README.md

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

• The program requires Python 3.7+. You can get the newest version of python by installing Anaconda (https://www.anaconda.com). To check your version of python, type

  python --version
  

  • Install or update all packages listed in 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

• 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.