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@@ -22,58 +22,32 @@ For detailed parameter and output description go to the [automatic segmentation
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## How to setup the environment
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Below is a quick guide to setup the enviroment on a UNIX (Mac and Linux) system
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-* 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
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- ```sh
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- python --version
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- ```
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-
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-* Install or update all packages listed in `requirements.txt`. All packages can be installed/updated using `pip`. To install a package, e.g. nibabel:
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-
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- ```sh
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- pip install nibabel
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- ```
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-
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- To check the version of a package
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- ```sh
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- pip freeze | grep nibabel
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- ```
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-* Install ANTs, preferably using precompiled binaries, available (for Mac/Linux) at
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- https://github.com/ANTsX/ANTs/releases/tag/v2.1.0
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-
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-* 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
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- ```sh
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- ~/.bashrc
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- ```
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- or
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- ```sh
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- ~/.bash_profile
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- ```
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-
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- In the config-file add the following lines
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- ```sh
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- export ANTSPATH=usr/local/bin/ANTs
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- export PATH=$PATH:$ANTSPATH
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- ```
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- Here, ANTs was installed in `/usr/local/bin/ANTs`
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-
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- After adding this to the config-file, restart the terminal and test if the
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- path was added correctly by typing
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- ```sh
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- which antsRegistration
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- ```
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- The correct path should then be printed.
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-
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-
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-* if permission is denied, the file needs to be made executable - this is done using the command
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- ```sh
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- chmod +x <...>/antsRegistration
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- ```
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-
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-
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+* 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```
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+* 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```
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+* Install ANTs, preferably using precompiled binaries, available (for Mac/Linux) at [https://github.com/ANTsX/ANTs/releases/tag/v2.1.0](https://github.com/ANTsX/ANTs/releases/tag/v2.1.0)
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+* 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
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+ ```sh
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+ export ANTSPATH=usr/local/bin/ANTs
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+ export PATH=$PATH:$ANTSPATH
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+ ```
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+ Here, ANTs was installed in ```/usr/local/bin/ANTs```.
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+
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+ After adding this to the config-file, restart the terminal and test if the path was added correctly by typing
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+ ```sh
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+ which antsRegistration
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+ ```
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+ 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```
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+
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+
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+
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## Prerequisites
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* A high-resolution, DAPI modality TIFF image of a coronal mouse brain slice. Can have multiple channels.
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* The DAPI template file (.nii or .nii.gz)
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-* A segmentation of the DAPI template (.nii or .nii.gz)
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-
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+* A segmentation of the DAPI template (.nii or .nii.gz)
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+
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+
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+
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## Usage
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-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](./automatic_segmentation_program).
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+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](./automatic_segmentation_program).
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+
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+
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