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.