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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.

datacite.yml
Title	Example Title
Authors	Stæger,Frederik Filip;Affiliation1;ORCID:0000-0001-2345-6789 FamilyName2,GivenName2;Affiliation2;ResearcherID:X-1234-5678 FamilyName3,GivenName3
Description	Example description that can contain linebreaks but has to maintain indentation.
License	Creative Commons CC0 1.0 Public Domain Dedication (https://creativecommons.org/publicdomain/zero/1.0/)
References	PublicationName1 [doi:10.xxx/zzzz] (IsSupplementTo) PublicationName2 [arxiv:mmmm.nnnn] (IsSupplementTo) PublicationName3 [pmid:nnnnnnnn] (IsReferencedBy)
Funding	DFG, DFG.12345 EU, EU.12345
Keywords	Neuroscience Electrophysiology
Resource Type	Dataset