Detail of ImageProcessingResult_D1BN_TM13.5_G
Project
Title
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)
Description
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)
Release, Updated
2023-05-09,
2023-05-29
2023-05-29
Errata in Project
2023/05/29 All BDML/BD5 data was updated cause of some format error in BD5
License
CC-BY
Kind
Quantitative data
based on Experiment
, related Image data -
D1BN_TM13.5_G
File Formats
BDML/BD5
Data size
7.7 GB
Organism
Mus musculus
(
NCBITaxon:10090
)
Strain(s)
C57BL/6 Neurod1^{CreER}(D1B); Tau^{mGFP-nLacZ}
Cell Line
-
Datatype
-
Molecular Function (MF)
Biological Process (BP)
nervous system development
(
GO:0007399
)
Cellular Component (CC)
plasma membrane
(
GO:0005886
)
neuron projection
(
GO:0043005
)
Biological Imaging Method
bright-field microscopy
(
Fbbi:00000243
)
chemically fixed tissue ( Fbbi:00000002 )
cryostat-sectioned tissue ( Fbbi:00000027 )
horseradish peroxidase ( Fbbi:00000138 )
chemically fixed tissue ( Fbbi:00000002 )
cryostat-sectioned tissue ( Fbbi:00000027 )
horseradish peroxidase ( Fbbi:00000138 )
X scale
1.0 micrometer/pixel
Y scale
1.0 micrometer/pixel
Z scale
20 micrometer/slice
T scale
-
Image Acquisition
Experiment type
-
Microscope type
-
Acquisition mode
-
Contrast method
-
Microscope model
-
Detector model
-
Objective model
-
Filter set
-
Summary of Methods
See details in Kawabata H, et. al. (2023) ICBET2023
Related paper(s)
Kawabata, Hiroto, Shimojo, Yuki, Hirata, Tatsumi, Tohsato, Yukako (2023) Large-scale Image Processing and Three-Dimensional Reconstruction of Mouse Brains with Neurogenic-Tagged Neurons, 1-7
Published in Dec. 19, 2023
(Abstract) The NeuroGT (neurogenic tagging) database provides images of whole-brain sections of mice in which neurons that differentiated at a similar time have been genetically tagged. The images of brain sections are displayed in order from the anterior to the posterior end on a web-browser, and the regions containing tagged neurons can be visually confirmed. However, it has been difficult to grasp their location in three-dimensional (3D) space. As a first step toward quantitative analysis of neuronal location, we automatically detected regions of mouse brains containing tagged neurons by using image processing and integrated that information into 3D space. We confirmed that the proposed methods detected brain regions with an average precision of 88% and average recall of 99%. We achieved visualization of 3D reconstructed brain shapes and distribution of tagged neurons in the regions of the brain.
Contact
Yukako Tohsato
, Ritsumeikan University
, Faculty of Information Science and Engineering
, Laboratory of compubational biology
Contributors
Hiroto Kawabata, Yuki Shimojo, Tatsumi Hirata, Yukako Tohsato
Local ID
ImageProcessingResult_D1BN_TM13.5_G
BDML ID
ab397c56-c7cf-4777-9760-3858dcb715e1
BDML/BD5
Database Link
Source