A three-dimensional, population-based average of the C57BL/6 mouse brain from DAPI-stained coronal slices
Research output: Contribution to journal › Journal article › Research › peer-review
Standard
A three-dimensional, population-based average of the C57BL/6 mouse brain from DAPI-stained coronal slices. / Stæger, Frederik Filip; Mortensen, Kristian Nygaard; Nielsen, Malthe Skytte Nordentoft; Sigurdsson, Björn; Kaufmann, Louis Krog; Hirase, Hajime; Nedergaard, Maiken.
In: Scientific Data, Vol. 7, No. 1, 235, 2020.Research output: Contribution to journal › Journal article › Research › peer-review
Harvard
APA
Vancouver
Author
Bibtex
}
RIS
TY - JOUR
T1 - A three-dimensional, population-based average of the C57BL/6 mouse brain from DAPI-stained coronal slices
AU - Stæger, Frederik Filip
AU - Mortensen, Kristian Nygaard
AU - Nielsen, Malthe Skytte Nordentoft
AU - Sigurdsson, Björn
AU - Kaufmann, Louis Krog
AU - Hirase, Hajime
AU - Nedergaard, Maiken
PY - 2020
Y1 - 2020
N2 - Fluorescence imaging of immunolabeled brain slices is a key tool in neuroscience that enable mapping of proteins or DNA/RNA at resolutions not possible with non-invasive techniques, including magnetic resonance or nuclear imaging. The signal in specific regions is usually quantified after manually drawing regions of interest, risking operator-bias. Automated segmentation methods avoid this risk but require multi-sample average atlases with similar image contrast as the images to be analyzed. We here present the first population-based average atlas of the C57BL/6 mouse brain constructed from brain sections labeled with the fluorescence nuclear stain DAPI. The data set constitutes a rich three-dimensional representation of the average mouse brain in the DAPI staining modality reconstructed from coronal slices and includes an automatic segmentation/spatial normalization pipeline for novel coronal slices. It constitutes the final population-based average template, individual reconstructed brain volumes, and native coronal slices. The comprehensive data set and accompanying spatial normalization/segmentation software are provided. We encourage the community to utilize it to improve and validate methods for automated brain slice analysis.
AB - Fluorescence imaging of immunolabeled brain slices is a key tool in neuroscience that enable mapping of proteins or DNA/RNA at resolutions not possible with non-invasive techniques, including magnetic resonance or nuclear imaging. The signal in specific regions is usually quantified after manually drawing regions of interest, risking operator-bias. Automated segmentation methods avoid this risk but require multi-sample average atlases with similar image contrast as the images to be analyzed. We here present the first population-based average atlas of the C57BL/6 mouse brain constructed from brain sections labeled with the fluorescence nuclear stain DAPI. The data set constitutes a rich three-dimensional representation of the average mouse brain in the DAPI staining modality reconstructed from coronal slices and includes an automatic segmentation/spatial normalization pipeline for novel coronal slices. It constitutes the final population-based average template, individual reconstructed brain volumes, and native coronal slices. The comprehensive data set and accompanying spatial normalization/segmentation software are provided. We encourage the community to utilize it to improve and validate methods for automated brain slice analysis.
KW - ATLASES
KW - SEGMENTATION
U2 - 10.1038/s41597-020-0570-z
DO - 10.1038/s41597-020-0570-z
M3 - Journal article
C2 - 32661243
VL - 7
JO - Scientific data
JF - Scientific data
SN - 2052-4463
IS - 1
M1 - 235
ER -
ID: 246632313