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B6_dapi_template
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10.12751/g-node.16wrxa
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Frederik Filip Stæger 29ee819fbd gin commit from SUND33778 4 years ago
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README.md

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

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 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
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
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
Funding
Keywords Neuroscience
Mouse brain template
C57BL/6 brain template
DAPI
Population-based average
Automatic segementation
Resource Type Dataset