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B6_dapi_template
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README_EXAMPLE.md

Example of the runner.py

How to run: In the command line 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 brain slice.

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
Nielsen,Malthe Skytte Nordentoft;Center for Translational Neuromedicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark;ORCID:0000-0002-7833-5877
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
Kaufmann,Louis;Center for Translational Neuromedicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
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