# Description
This repository contains the full data set for constructing the DAPI template, the full DAPI template creation pipeline and the automatic slice segmentation.

# Automatic slice segmentation
Program for automatic segmentation to a DAPI-stained coronal mouse brain slices.

## Dependencies
* Python 3.6
* Ants (https://github.com/ANTsX/ANTs)

## Prerequisites
* A high-resolution, DAPI modality TIFF image of a brain slice. Can have multiple channels.
* A template file (.nii or .nii.gz)
* A segmentation of the template file  (.nii or .nii.gz)

## Usage:
* Use preprocess.py to prepare input slice for automatic registration
* Use auto_seg.py with preprocessed slice which will output a folder containing segmentation registered to slice.