296-Kawabata-MouseBrainShape
Author reviewedImage processing and manual annotation data of mouse brains with neurogenic-tagged neurons from NeuroGT database
Project ID
296-Kawabata-MouseBrainShape
Title
Image processing and manual annotation data of mouse brains with neurogenic-tagged neurons from NeuroGT database
Description
Segmentation results of brain contours and tagged neurons for 84 imaging data sets provied from NeuroGT database and manual annotation data of anatomical regions (isocortex, olfactory area, hippocampal formation, cerebral nuclei, interbrain, midbrain, hindbrain, and cerebellum) for images (131 images for the G2AN_TM11.5_L dataset and 10 images each for the other datasets) targetd mouse brains for evaluation
Release Date
2023-05-09
Update Date
2023-05-29
License
Version
1.0.0
Method Summary
See details in Kawabata H, et. al. (2023) ICBET2023
Paper DOI
-
Paper URL
-
Kind
Image data
Quantitative data
Total
2337 files / 3.5 TB
Image datasets
zipped 84 files / 1.6 TB, raw image 1245 files / 1.6 TB, total 1329 files / 3.3 TB
Quantitative datasets
zipped 168 files / 6.6 GB, raw bdml 336 files / 100.2 GB, total 504 files / 106.9 GB
Organism
Mus musculus
(
NCBITaxon:10090
)
Strain
C57BL/6
Neurod1CreER(D1B); TaumGFP-nLacZ
C57BL/6 Neurod1^{CreER}(D1B); Tau^{mGFP-nLacZ}
Neurod4CreER(D4A); TaumGFP-nLacZ
C57BL/6 Neurod4^{CreER}(D4A); Tau^{mGFP-nLacZ}
Cell line
-
Biological Process
nervous system development
(
GO:0007399
)
Cellular Component
plasma membrane
(
GO:0005886
)
neuron projection
(
GO:0043005
)
nucleus
(
GO:0005634
)
cell body
(
GO:0044297
)
Medical Subject Headings
neurons
(
MeSH:D009474
)
axons
(
MeSH:D001369
)
brain
(
MeSH:D001921
)
mice transgenic
(
MeSH:D008822
)
immunohistochemistry
(
MeSH:D007150
)
cell body
(
MeSH:D066146
)
Method involved in biological imaging
bright-field microscopy
(
FBbi:00000243
)
chemically fixed tissue
(
FBbi:00000002
)
cryostat-sectioned tissue
(
FBbi:00000027
)
horseradish peroxidase
(
FBbi:00000138
)
Image datasets
168
Quantitative datasets
168
Paper DOI / Paper URL
Kawabata H, Shimojo Y, Hirata T, Tohsato Y (2023) Large-scale image processing and three-dimensional reconstruction of mouse brains with neurogenic-tagged neurons
OMERO.gallery
People
Contact
Yukako Tohsato
Ritsumeikan University
Faculty of Information Science and Engineering
Laboratory of compubational biology
1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577 Japan
Imaging dataset contributor
-
Quantitative dataset contributor
Hiroto Kawabata
(Ritsumeikan University)
Yuki Shimojo
(Ritsumeikan University)
Tatsumi Hirata
(National Institute of Genetics)
Yukako Tohsato
(Ritsumeikan University)
Datasets
Thumbnail
Dataset
Organism
Kind / Links
Mus musculus
(
NCBITaxon:10090
)
brain sections of a P7 mouse (ID:N3) that was birthdate tagged at E10.5 (TM10.5) and visualized for membrane-localized GFP reporter
BDML file for segmentation results of brain contours and tagged neurons for all images of P7 mouse brains (D1BN_TM10.5_G dataset) that was neurogenic-tagged at E10.5 and was visualied for membrane-localized GFP reporter (G)
Mus musculus
(
NCBITaxon:10090
)
brain sections of a P7 mouse (ID:N3) that was birthdate tagged at E10.5 (TM10.5) and visualized for nucleus-localized beta-galactosidase reporter
BDML file for segmentation results of brain contours and tagged neurons for all images of P7 mouse brains (D1BN_TM10.5_L dataset) that was neurogenic-tagged at E10.5 and was visualied for nucleus-localized beta-galactosidase reporter (L)
Mus musculus
(
NCBITaxon:10090
)
brain sections of a P7 mouse (ID:N6) that was birthdate tagged at E11.5 (TM11.5) and visualized for membrane-localized GFP reporter
BDML file for segmentation results of brain contours and tagged neurons for all images of P7 mouse brains (D1BN_TM11.5_G dataset) that was neurogenic-tagged at E11.5 and was visualied for membrane-localized GFP reporter (G)
Mus musculus
(
NCBITaxon:10090
)
brain sections of a P7 mouse (ID:N6) that was birthdate tagged at E11.5 (TM11.5) and visualized for nucleus-localized beta-galactosidase reporter
BDML file for segmentation results of brain contours and tagged neurons for all images of P7 mouse brains (D1BN_TM11.5_L dataset) that was neurogenic-tagged at E11.5 and was visualied for nucleus-localized beta-galactosidase reporter (L)
Mus musculus
(
NCBITaxon:10090
)
brain sections of a P7 mouse (ID:2) that was birthdate tagged at E12.5 (TM12.5) and visualized for membrane-localized GFP reporter
BDML file for segmentation results of brain contours and tagged neurons for all images of P7 mouse brains (D1BN_TM12.5_G dataset) that was neurogenic-tagged at E12.5 and was visualied for membrane-localized GFP reporter (G)
Mus musculus
(
NCBITaxon:10090
)
brain sections of a P7 mouse (ID:2) that was birthdate tagged at E12.5 (TM12.5) and visualized for nucleus-localized beta-galactosidase reporter
BDML file for segmentation results of brain contours and tagged neurons for all images of P7 mouse brains (D1BN_TM12.5_L dataset) that was neurogenic-tagged at E12.5 and was visualied for nucleus-localized beta-galactosidase reporter (L)
Mus musculus
(
NCBITaxon:10090
)
brain sections of a P7 mouse (ID:N6) that was birthdate tagged at E13.5 (TM13.5) and visualized for membrane-localized GFP reporter
BDML file for segmentation results of brain contours and tagged neurons for all images of P7 mouse brains (D1BN_TM13.5_G dataset) that was neurogenic-tagged at E13.5 and was visualied for membrane-localized GFP reporter (G)
Mus musculus
(
NCBITaxon:10090
)
brain sections of a P7 mouse (ID:N6) that was birthdate tagged at E13.5 (TM13.5) and visualized for nucleus-localized beta-galactosidase reporter
BDML file for segmentation results of brain contours and tagged neurons for all images of P7 mouse brains (D1BN_TM13.5_L dataset) that was neurogenic-tagged at E13.5 and was visualied for nucleus-localized beta-galactosidase reporter (L)
Mus musculus
(
NCBITaxon:10090
)
brain sections of a P7 mouse (ID:N4) that was birthdate tagged at E14.5 (TM14.5) and visualized for membrane-localized GFP reporter
BDML file for segmentation results of brain contours and tagged neurons for all images of P7 mouse brains (D1BN_TM14.5_G dataset) that was neurogenic-tagged at E14.5 and was visualied for membrane-localized GFP reporter (G)
Mus musculus
(
NCBITaxon:10090
)
brain sections of a P7 mouse (ID:N4) that was birthdate tagged at E14.5 (TM14.5) and visualized for nucleus-localized beta-galactosidase reporter
BDML file for segmentation results of brain contours and tagged neurons for all images of P7 mouse brains (D1BN_TM14.5_L dataset) that was neurogenic-tagged at E14.5 and was visualied for nucleus-localized beta-galactosidase reporter (L)
Mus musculus
(
NCBITaxon:10090
)
brain sections of a P7 mouse (ID:N5) that was birthdate tagged at E15.5 (TM15.5) and visualized for membrane-localized GFP reporter
BDML file for segmentation results of brain contours and tagged neurons for all images of P7 mouse brains (D1BN_TM15.5_G dataset) that was neurogenic-tagged at E15.5 and was visualied for membrane-localized GFP reporter (G)
Mus musculus
(
NCBITaxon:10090
)
brain sections of a P7 mouse (ID:N5) that was birthdate tagged at E15.5 (TM15.5) and visualized for nucleus-localized beta-galactosidase reporter
BDML file for segmentation results of brain contours and tagged neurons for all images of P7 mouse brains (D1BN_TM15.5_L dataset) that was neurogenic-tagged at E15.5 and was visualied for nucleus-localized beta-galactosidase reporter (L)
Mus musculus
(
NCBITaxon:10090
)
brain sections of a P7 mouse (ID:1) that was birthdate tagged at E16.5 (TM16.5) and visualized for membrane-localized GFP reporter
BDML file for segmentation results of brain contours and tagged neurons for all images of P7 mouse brains (D1BN_TM16.5_G dataset) that was neurogenic-tagged at E16.5 and was visualied for membrane-localized GFP reporter (G)
Mus musculus
(
NCBITaxon:10090
)
brain sections of a P7 mouse (ID:1) that was birthdate tagged at E16.5 (TM16.5) and visualized for nucleus-localized beta-galactosidase reporter
BDML file for segmentation results of brain contours and tagged neurons for all images of P7 mouse brains (D1BN_TM16.5_L dataset) that was neurogenic-tagged at E16.5 and was visualied for nucleus-localized beta-galactosidase reporter (L)
Mus musculus
(
NCBITaxon:10090
)
brain sections of a P7 mouse (ID:1) that was birthdate tagged at E17.5 (TM17.5) and visualized for membrane-localized GFP reporter
BDML file for segmentation results of brain contours and tagged neurons for all images of P7 mouse brains (D1BN_TM17.5_G dataset) that was neurogenic-tagged at E17.5 and was visualied for membrane-localized GFP reporter (G)
Mus musculus
(
NCBITaxon:10090
)
brain sections of a P7 mouse (ID:1) that was birthdate tagged at E17.5 (TM17.5) and visualized for nucleus-localized beta-galactosidase reporter
BDML file for segmentation results of brain contours and tagged neurons for all images of P7 mouse brains (D1BN_TM17.5_L dataset) that was neurogenic-tagged at E17.5 and was visualied for nucleus-localized beta-galactosidase reporter (L)
Mus musculus
(
NCBITaxon:10090
)
brain sections of a P7 mouse (ID:N4) that was birthdate tagged at E9.5 (TM9.5) and visualized for membrane-localized GFP reporter
BDML file for segmentation results of brain contours and tagged neurons for all images of P7 mouse brains (D1BN_TM9.5_G dataset) that was neurogenic-tagged at E9.5 and was visualied for membrane-localized GFP reporter (G)
Mus musculus
(
NCBITaxon:10090
)
brain sections of a P7 mouse (ID:N4) that was birthdate tagged at E9.5 (TM9.5) and visualized for nucleus-localized beta-galactosidase reporter
BDML file for segmentation results of brain contours and tagged neurons for all images of P7 mouse brains (D1BN_TM9.5_L dataset) that was neurogenic-tagged at E9.5 and was visualied for nucleus-localized beta-galactosidase reporter (L)
Mus musculus
(
NCBITaxon:10090
)
brain sections of a P8 mouse (ID:1) without a TM injection (woTM) stained for membrane-localized GFP reporter
BDML file for segmentation results of brain contours and tagged neurons for all images of P8 mouse brains (D1BN_woTM_G dataset) that was not injected TM (woTM) and was visualied for membrane-localized GFP reporter (G)
Mus musculus
(
NCBITaxon:10090
)
brain sections of a P8 mouse (ID:1) without a TM injection (woTM) stained for nucleus-localized beta-galactosidase reporter
BDML file for segmentation results of brain contours and tagged neurons for all images of P8 mouse brains (D1BN_woTM_L dataset) that was not injected TM (woTM) and was visualied for nucleus-localized beta-galactosidase reporter (L)
Mus musculus
(
NCBITaxon:10090
)
brain sections of a P7 mouse (ID:1) that was birthdate tagged at E10.5 (TM10.5) and visualized for membrane-localized GFP reporter
BDML file for segmentation results of brain contours and tagged neurons for all images of P7 mouse brains (D4AN_TM10.5_G dataset) that was neurogenic-tagged at E10.5 and was visualied for membrane-localized GFP reporter (G)
Mus musculus
(
NCBITaxon:10090
)
brain sections of a P7 mouse (ID:1) that was birthdate tagged at E10.5 (TM10.5) and visualized for nucleus-localized beta-galactosidase reporter
BDML file for segmentation results of brain contours and tagged neurons for all images of P7 mouse brains (D4AN_TM10.5_L dataset) that was neurogenic-tagged at E10.5 and was visualied for nucleus-localized beta-galactosidase reporter (L)
Mus musculus
(
NCBITaxon:10090
)
brain sections of a P7 mouse (ID:1) that was birthdate tagged at E11.5 (TM11.5) and visualized for membrane-localized GFP reporter
BDML file for segmentation results of brain contours and tagged neurons for all images of P7 mouse brains (D4AN_TM11.5_G dataset) that was neurogenic-tagged at E11.5 and was visualied for membrane-localized GFP reporter (G)
Mus musculus
(
NCBITaxon:10090
)
brain sections of a P7 mouse (ID:1) that was birthdate tagged at E11.5 (TM11.5) and visualized for nucleus-localized beta-galactosidase reporter
BDML file for segmentation results of brain contours and tagged neurons for all images of P7 mouse brains (D4AN_TM11.5_L dataset) that was neurogenic-tagged at E11.5 and was visualied for nucleus-localized beta-galactosidase reporter (L)
Mus musculus
(
NCBITaxon:10090
)
brain sections of a P7 mouse (ID:1) that was birthdate tagged at E12.5 (TM12.5) and visualized for membrane-localized GFP reporter
BDML file for segmentation results of brain contours and tagged neurons for all images of P7 mouse brains (D4AN_TM12.5_G dataset) that was neurogenic-tagged at E12.5 and was visualied for membrane-localized GFP reporter (G)