CTN/B6_dapi_template @ 061ea5ee3dd0e40f49f2b63dac3f21013444e7e6

malthe.nielsen 061ea5ee3d gin commit from rMBP-15-Malthe.local		%!s(int64=4) %!d(string=hai) anos
..
.gitignore	061ea5ee3d gin commit from rMBP-15-Malthe.local	%!s(int64=4) %!d(string=hai) anos
README_EXAMPLE.txt	061ea5ee3d gin commit from rMBP-15-Malthe.local	%!s(int64=4) %!d(string=hai) anos
runner_example.sh	061ea5ee3d gin commit from rMBP-15-Malthe.local	%!s(int64=4) %!d(string=hai) anos
runner_example_macOS.sh	061ea5ee3d gin commit from rMBP-15-Malthe.local	%!s(int64=4) %!d(string=hai) anos

		
				README_EXAMPLE.txt
			
		In this folder an example of the automatic segementation program shown.

By running one of the two shell scripts the program starts and segments a
brainslice with the segmentation and template files. There are two diffrent
scripts, one for MacOS and one for Linux. The only difference between the two is
in the nameing of the python instalation. The program only works with python
3.7+ and the default macOS instalation of python is 2.7. You are able to check
the version of your python instalation by typing 'python --version' in the
command line. If the version installed is python 2.7 the python 3 package is
often installed as 'python3' instead 

How to run:
In the commandline type in 'bash runner_example.sh'

The program will run the program with the sample file and output the correct
files in a new directory inside this one named after the file name of the
brainslice.

datacite.yml
Title	A three-dimensional, population-based average of the C57BL/6 mouse brain from DAPI-stained coronal slices
Authors	Stæger,Frederik Filip;Center for Translational Neuromedicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark;ORCID:0000-0002-2295-8637 Mortensen,Kristian;Center for Translational Neuromedicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark;ORCID:0000-0003-3726-0781 Kaufmann,Louis;Center for Translational Neuromedicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark Hirase,Hajime;Center for Translational Neuromedicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark;ORCID:0000-0003-3806-6905 Sigurdsson,Björn;Center for Translational Neuromedicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark;ORCID:0000-0002-7484-7779 Nedergaard,Maiken;Center for Translational Neuromedicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark and Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642, USA.;ORCID:0000-0001-6502-6031
Description	The full data set and pipeline for constructing the three-dimensional, population-based average of the C57BL/6 mouse brain form DAPI-stained coronal slices. This repository also contains a python implementation of automatic coronal brain slice segmentation. The data set constitutes of all the raw slice images (.tif) in full resolution, the pre-processed version (.nii), the individually reconstructed brain volumes, and the final population-based average.
License	Creative Commons CC0 1.0 Public Domain Dedication (https://creativecommons.org/publicdomain/zero/1.0/)
References	A three-dimensional, population-based average of the C57BL/6 mouse brain from DAPI-stained coronal slices [] (IsDescribedBy)
Funding
Keywords	Neuroscience Mouse brain template C57BL/6 brain template DAPI Population-based average Automatic segementation
Resource Type	Dataset