Frederik Filip Stæger
b540578164
gin commit from SUND33778
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5 年 前 | |
|---|---|---|
| data | 5 年 前 | |
| template_creation_pipeline | 5 年 前 | |
| LICENSE | 5 年 前 | |
| README.md | 5 年 前 | |
| auto_seg.py | 5 年 前 | |
| datacite.yml | 5 年 前 | |
| preprocess.py | 5 年 前 | |
| registration.py | 5 年 前 | |
| requirements.txt | 5 年 前 | |
| tools.py | 5 年 前 |
# Description This repository contains the full data set for constructing the DAPI template, the full DAPI template creation pipeline and the automatic slice segmentation.
Program for automatic segmentation to a DAPI-stained coronal mouse brain slices.
Usage
python3 auto_seg.py sliceloc segloc templateloc --bregma [coord]
Positional/Required Arguments
sliceloc |
Location of the slice you wish to register (.nii or.nii.gz) |
segloc |
Location of file containing segmentation of the template (.nii or.nii.gz) |
templateloc |
Location of template file (.nii or .nii.gz) |
--bregma [coord] |
Bregma coordinate of input slice (if --approx argument is present, this is an optional argument) |
Optional arguments
--approx [index] |
Provide the location of the slice as a z-index of the template. Can be used instead of --bregma argument. |
--out [directory] |
Provide an alternative output directory (default directory is /output) |
--dapi [index] |
Index of the DAPI channel in the slice, by default the DAPI channel is assumed to be the last channel |
Usage
python3 preprocess.py file dir -s Series -b [True/False] --pdim [pixeldimension]
Positional/Required Arguments
file |
Location of the file to be preprocessed (.tiff or .nd2) |
dir |
Directory to output preprocessed files (will output .nii files) |
-s |
The series to extract (If input file is single-series, use 0 for this argument) |
Optional arguments
--b [True/False] |
Bias field correction: Whether to use bias-field correction in preprocessing (default: True) |
--pdim [pixeldimensions] |
Dimensions of pixels, if not provided, these will be extracted from image metadata |
| 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 |