Automatic slice segmentation

Program for automatically registering a segmentation to a DAPI-stained slice.

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.