Summary of 331-Shimojo-MouseBrainAnatomicalRegion

SSBD:database
SSBD:database URL
DOI
Title
Semantic segmentation data of eight anatomical regions for mouse brain slices with neurogenic-tagged neurons from NeuroGT database
Description
-
Relase date
2023-12-24
Updated date
-
License
CC BY
Kind
Quantitative data based on Experiment
Number of Datasets
84 ( Image datasets: 0, Quantitative data datasets: 84 )
Size of Datasets
52.4 GB ( Image datasets: 0 bytes, Quantitative data datasets: 52.4 GB )

Organism(s)
Mus musculus
Strain(s)
C57BL/6 Neurog1^{CreER}(G1C); Tau^{mGFP-nLacZ}, C57BL/6 Neurod1^{CreER}(D1B); Tau^{mGFP-nLacZ}, C57BL/6 neuroG2^{CreER}(G2A); Tau^{mGFP-nLacZ}, C57BL/6 Neurod4^{CreER}(D4A); Tau^{mGFP-nLacZ}
Gene symbol(s)
NA
Protein name(s)
NA

Datatype
-
Molecular Function (MF)
-
Biological Process (BP)
nervous system development
Cellular Component (CC)
plasma membrane, neuron projection
Biological Imaging Method
-
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
-

Related paper(s)

Shimojo,Yuki, Suehara,Kazuki, Hirata,Tatsumi, Tohsato,Yukako (2024) Segmentation of Mouse Brain Slices with Unsupervised Domain Adaptation Considering Cross-sectional Locations, IPSJ Transactions on Bioinformatics, Volume 17, Number , 33-39

Published in 2024

(Abstract) Images of mouse brain slices, obtained under slightly different experimental conditions, are available in 84 datasets in the NeuroGT database (https://ssbd.riken.jp/neurogt/). Our goal was to obtain semantic segmentation results for eight brain anatomical regions. However, out of 84 datasets, only one dataset had true labels that could be used to train a convolutional neural network (CNN), and it was incomplete (131 out of 162 images). A segmentation model trained with the labeled images was less accurate on other images obtained under different experimental conditions because of differences of the image properties. We therefore tried Unsupervised Domain Adaptation (UDA), wherein the parameters of the CNN trained on the labeled images (source) were transferred to the unlabeled images (target). We used the positional information of the sample slices associated with each image to propose a novel loss function that approximated the class occurrence probabilities of segmentation results obtained from source and target images of brain samples at similar sliced locations, and we introduced it into the UDA. The proposed UDA method achieved an mIoU of 78.34%, which was 8% more accurate than the previous UDA methods such as Contrastive Learning and Self-Training (CLST) and Maximum Classifier Discrepancy (MCD). We demonstrated experimentally that the proposed method was useful for segmenting biomedical images with a small amount of incomplete training data.

Contact
Yukako Tohsato , Ritsumeikan University , Faculty of Information Science and Engineering , Laboratory of compubational biology
Contributors
Yuki Shimojo, Kazuki Suehara, Tatsumi Hirata, Yukako Tohsato


Dataset List of 331-Shimojo-MouseBrainAnatomicalRegion

#
Dataset ID
Kind
Size
4D View
SSBD:OMERO
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# 11009
Datast ID D1BN_TM9.5_G
Dataset Kind Quantitative data
Dataset Size 594.4 MB
4D view
SSBD:OMERO
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# 11010
Datast ID D1BN_TM9.5_L
Dataset Kind Quantitative data
Dataset Size 624.5 MB
4D view
SSBD:OMERO
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# 11011
Datast ID D1BN_TM10.5_G
Dataset Kind Quantitative data
Dataset Size 571.4 MB
4D view
SSBD:OMERO
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# 11012
Datast ID D1BN_TM10.5_L
Dataset Kind Quantitative data
Dataset Size 510.2 MB
4D view
SSBD:OMERO
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# 11013
Datast ID D1BN_TM11.5_G
Dataset Kind Quantitative data
Dataset Size 565.9 MB
4D view
SSBD:OMERO
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# 11014
Datast ID D1BN_TM11.5_L
Dataset Kind Quantitative data
Dataset Size 561.5 MB
4D view
SSBD:OMERO
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# 11015
Datast ID D1BN_TM12.5_G
Dataset Kind Quantitative data
Dataset Size 655.7 MB
4D view
SSBD:OMERO
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# 11016
Datast ID D1BN_TM12.5_L
Dataset Kind Quantitative data
Dataset Size 636.0 MB
4D view
SSBD:OMERO
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# 11017
Datast ID D1BN_TM13.5_G
Dataset Kind Quantitative data
Dataset Size 580.9 MB
4D view
SSBD:OMERO
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# 11018
Datast ID D1BN_TM13.5_L
Dataset Kind Quantitative data
Dataset Size 611.1 MB
4D view
SSBD:OMERO
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# 11019
Datast ID D1BN_TM14.5_G
Dataset Kind Quantitative data
Dataset Size 581.1 MB
4D view
SSBD:OMERO
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# 11020
Datast ID D1BN_TM14.5_L
Dataset Kind Quantitative data
Dataset Size 579.2 MB
4D view
SSBD:OMERO
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# 11021
Datast ID D1BN_TM15.5_G
Dataset Kind Quantitative data
Dataset Size 603.4 MB
4D view
SSBD:OMERO
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# 11022
Datast ID D1BN_TM15.5_L
Dataset Kind Quantitative data
Dataset Size 587.1 MB
4D view
SSBD:OMERO
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# 11023
Datast ID D1BN_TM16.5_G
Dataset Kind Quantitative data
Dataset Size 778.9 MB
4D view
SSBD:OMERO
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# 11024
Datast ID D1BN_TM16.5_L
Dataset Kind Quantitative data
Dataset Size 672.4 MB
4D view
SSBD:OMERO
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# 11025
Datast ID D1BN_TM17.5_G
Dataset Kind Quantitative data
Dataset Size 708.4 MB
4D view
SSBD:OMERO
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# 11026
Datast ID D1BN_TM17.5_L
Dataset Kind Quantitative data
Dataset Size 700.5 MB
4D view
SSBD:OMERO
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# 11027
Datast ID D1BN_woTM_G
Dataset Kind Quantitative data
Dataset Size 634.8 MB
4D view
SSBD:OMERO
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# 11028
Datast ID D1BN_woTM_L
Dataset Kind Quantitative data
Dataset Size 634.9 MB
4D view
SSBD:OMERO
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# 11029
Datast ID D4AN_TM8.5_G
Dataset Kind Quantitative data
Dataset Size 655.9 MB
4D view
SSBD:OMERO
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# 11030
Datast ID D4AN_TM8.5_L
Dataset Kind Quantitative data
Dataset Size 655.7 MB
4D view
SSBD:OMERO
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# 11031
Datast ID D4AN_TM9.5_G
Dataset Kind Quantitative data
Dataset Size 692.0 MB
4D view
SSBD:OMERO
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# 11032
Datast ID D4AN_TM9.5_L
Dataset Kind Quantitative data
Dataset Size 694.9 MB
4D view
SSBD:OMERO
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# 11033
Datast ID D4AN_TM10.5_G
Dataset Kind Quantitative data
Dataset Size 575.1 MB
4D view
SSBD:OMERO
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# 11034
Datast ID D4AN_TM10.5_L
Dataset Kind Quantitative data
Dataset Size 572.3 MB
4D view
SSBD:OMERO
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# 11035
Datast ID D4AN_TM11.5_G
Dataset Kind Quantitative data
Dataset Size 653.3 MB
4D view
SSBD:OMERO
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# 11036
Datast ID D4AN_TM11.5_L
Dataset Kind Quantitative data
Dataset Size 628.3 MB
4D view
SSBD:OMERO
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# 11037
Datast ID D4AN_TM12.5_G
Dataset Kind Quantitative data
Dataset Size 613.7 MB
4D view
SSBD:OMERO
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# 11038
Datast ID D4AN_TM12.5_L
Dataset Kind Quantitative data
Dataset Size 595.5 MB
4D view
SSBD:OMERO
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# 11039
Datast ID D4AN_TM13.5_G
Dataset Kind Quantitative data
Dataset Size 761.5 MB
4D view
SSBD:OMERO
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# 11040
Datast ID D4AN_TM13.5_L
Dataset Kind Quantitative data
Dataset Size 741.7 MB
4D view
SSBD:OMERO
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# 11041
Datast ID D4AN_TM14.5_G
Dataset Kind Quantitative data
Dataset Size 567.5 MB
4D view
SSBD:OMERO
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# 11042
Datast ID D4AN_TM14.5_L
Dataset Kind Quantitative data
Dataset Size 579.7 MB
4D view
SSBD:OMERO
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# 11043
Datast ID D4AN_TM15.5_G
Dataset Kind Quantitative data
Dataset Size 526.1 MB
4D view
SSBD:OMERO
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# 11044
Datast ID D4AN_TM15.5_L
Dataset Kind Quantitative data
Dataset Size 517.8 MB
4D view
SSBD:OMERO
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# 11045
Datast ID D4AN_TM16.5_G
Dataset Kind Quantitative data
Dataset Size 668.3 MB
4D view
SSBD:OMERO
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# 11046
Datast ID D4AN_TM16.5_L
Dataset Kind Quantitative data
Dataset Size 653.1 MB
4D view
SSBD:OMERO
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# 11047
Datast ID D4AN_TM17.5_G
Dataset Kind Quantitative data
Dataset Size 515.6 MB
4D view
SSBD:OMERO
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# 11048
Datast ID D4AN_TM17.5_L
Dataset Kind Quantitative data
Dataset Size 522.0 MB
4D view
SSBD:OMERO
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# 11049
Datast ID D4AN_woTM_G
Dataset Kind Quantitative data
Dataset Size 683.2 MB
4D view
SSBD:OMERO
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# 11050
Datast ID D4AN_woTM_L
Dataset Kind Quantitative data
Dataset Size 661.0 MB
4D view
SSBD:OMERO
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# 11051
Datast ID G1CN_TM9.5_G
Dataset Kind Quantitative data
Dataset Size 710.7 MB
4D view
SSBD:OMERO
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# 11052
Datast ID G1CN_TM9.5_L
Dataset Kind Quantitative data
Dataset Size 640.2 MB
4D view
SSBD:OMERO
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# 11053
Datast ID G1CN_TM10.5_G
Dataset Kind Quantitative data
Dataset Size 715.6 MB
4D view
SSBD:OMERO
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# 11054
Datast ID G1CN_TM10.5_L
Dataset Kind Quantitative data
Dataset Size 712.4 MB
4D view
SSBD:OMERO
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# 11055
Datast ID G1CN_TM11.5_G
Dataset Kind Quantitative data
Dataset Size 549.0 MB
4D view
SSBD:OMERO
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# 11056
Datast ID G1CN_TM11.5_L
Dataset Kind Quantitative data
Dataset Size 559.7 MB
4D view
SSBD:OMERO
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# 11057
Datast ID G1CN_TM12.5_G
Dataset Kind Quantitative data
Dataset Size 556.0 MB
4D view
SSBD:OMERO
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# 11058
Datast ID G1CN_TM12.5_L
Dataset Kind Quantitative data
Dataset Size 550.9 MB
4D view
SSBD:OMERO
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# 11059
Datast ID G1CN_TM13.5_G
Dataset Kind Quantitative data
Dataset Size 686.6 MB
4D view
SSBD:OMERO
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# 11060
Datast ID G1CN_TM13.5_L
Dataset Kind Quantitative data
Dataset Size 671.1 MB
4D view
SSBD:OMERO
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# 11061
Datast ID G1CN_TM14.5_G
Dataset Kind Quantitative data
Dataset Size 614.6 MB
4D view
SSBD:OMERO
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# 11062
Datast ID G1CN_TM14.5_L
Dataset Kind Quantitative data
Dataset Size 635.8 MB
4D view
SSBD:OMERO
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# 11063
Datast ID G1CN_TM15.5_G
Dataset Kind Quantitative data
Dataset Size 648.5 MB
4D view
SSBD:OMERO
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# 11064
Datast ID G1CN_TM15.5_L
Dataset Kind Quantitative data
Dataset Size 603.4 MB
4D view
SSBD:OMERO
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# 11065
Datast ID G1CN_TM16.5_G
Dataset Kind Quantitative data
Dataset Size 613.7 MB
4D view
SSBD:OMERO
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# 11066
Datast ID G1CN_TM16.5_L
Dataset Kind Quantitative data
Dataset Size 614.6 MB
4D view
SSBD:OMERO
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# 11067
Datast ID G1CN_TM17.5_G
Dataset Kind Quantitative data
Dataset Size 601.0 MB
4D view
SSBD:OMERO
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# 11068
Datast ID G1CN_TM17.5_L
Dataset Kind Quantitative data
Dataset Size 578.1 MB
4D view
SSBD:OMERO
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# 11069
Datast ID G1CN_woTM_G
Dataset Kind Quantitative data
Dataset Size 711.6 MB
4D view
SSBD:OMERO
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# 11070
Datast ID G1CN_woTM_L
Dataset Kind Quantitative data
Dataset Size 737.2 MB
4D view
SSBD:OMERO
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# 11071
Datast ID G2AN_TM9.5_G
Dataset Kind Quantitative data
Dataset Size 668.8 MB
4D view
SSBD:OMERO
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# 11072
Datast ID G2AN_TM9.5_L
Dataset Kind Quantitative data
Dataset Size 657.3 MB
4D view
SSBD:OMERO
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# 11073
Datast ID G2AN_TM10.5_G
Dataset Kind Quantitative data
Dataset Size 633.0 MB
4D view
SSBD:OMERO
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# 11074
Datast ID G2AN_TM10.5_L
Dataset Kind Quantitative data
Dataset Size 592.9 MB
4D view
SSBD:OMERO
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# 11075
Datast ID G2AN_TM11.5_G
Dataset Kind Quantitative data
Dataset Size 628.4 MB
4D view
SSBD:OMERO
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# 11076
Datast ID G2AN_TM11.5_L
Dataset Kind Quantitative data
Dataset Size 593.1 MB
4D view
SSBD:OMERO
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# 11077
Datast ID G2AN_TM12.5_G
Dataset Kind Quantitative data
Dataset Size 751.8 MB
4D view
SSBD:OMERO
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# 11078
Datast ID G2AN_TM12.5_L
Dataset Kind Quantitative data
Dataset Size 716.0 MB
4D view
SSBD:OMERO
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# 11079
Datast ID G2AN_TM13.5_G
Dataset Kind Quantitative data
Dataset Size 712.7 MB
4D view
SSBD:OMERO
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# 11080
Datast ID G2AN_TM13.5_L
Dataset Kind Quantitative data
Dataset Size 756.2 MB
4D view
SSBD:OMERO
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# 11081
Datast ID G2AN_TM14.5_G
Dataset Kind Quantitative data
Dataset Size 666.7 MB
4D view
SSBD:OMERO
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# 11082
Datast ID G2AN_TM14.5_L
Dataset Kind Quantitative data
Dataset Size 635.2 MB
4D view
SSBD:OMERO
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# 11083
Datast ID G2AN_TM15.5_G
Dataset Kind Quantitative data
Dataset Size 722.7 MB
4D view
SSBD:OMERO
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# 11084
Datast ID G2AN_TM15.5_L
Dataset Kind Quantitative data
Dataset Size 707.5 MB
4D view
SSBD:OMERO
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# 11085
Datast ID G2AN_TM16.5_G
Dataset Kind Quantitative data
Dataset Size 701.4 MB
4D view
SSBD:OMERO
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# 11086
Datast ID G2AN_TM16.5_L
Dataset Kind Quantitative data
Dataset Size 686.5 MB
4D view
SSBD:OMERO
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# 11087
Datast ID G2AN_TM17.5_G
Dataset Kind Quantitative data
Dataset Size 702.6 MB
4D view
SSBD:OMERO
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# 11088
Datast ID G2AN_TM17.5_L
Dataset Kind Quantitative data
Dataset Size 692.0 MB
4D view
SSBD:OMERO
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# 11089
Datast ID G2AN_TM18.5_G
Dataset Kind Quantitative data
Dataset Size 742.5 MB
4D view
SSBD:OMERO
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# 11090
Datast ID G2AN_TM18.5_L
Dataset Kind Quantitative data
Dataset Size 723.7 MB
4D view
SSBD:OMERO
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# 11091
Datast ID G2AN_woTM_G
Dataset Kind Quantitative data
Dataset Size 563.1 MB
4D view
SSBD:OMERO
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# 11092
Datast ID G2AN_woTM_L
Dataset Kind Quantitative data
Dataset Size 574.1 MB
4D view
SSBD:OMERO
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