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@@ -1,3 +1,4 @@
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# Description of DAPI template
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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](./data/dapi_template.nii.gz), [accompanying segmentation](./data/dapi_template_segmentation_full.nii.gz), and a [simplified segmentation](./data/dapi_template_segmentation_simple.nii.gz) 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.
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@@ -27,14 +28,15 @@ Below is a quick guide to setup the enviroment on a UNIX (Mac and Linux) system
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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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```sh
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pip install nibabel
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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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-
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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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