SSBD:database

Summary of 25-Ke-SeeDB

SSBD:database
25-Ke-SeeDB
SSBD:database URL
https://ssbd.riken.jp/database/25/
Title
-
Description
-
Relase date
2017-10-03
Updated date
2017-11-15
License
CC BY
Kind
Image data based on Experiment
Number of Datasets
52 ( Image datasets: 52, Quantitative data datasets: 0 )
Size of Datasets
17.1 GB ( Image datasets: 17.1 GB, Quantitative data datasets: 0 bytes )
Organism(s)
M. musculus
Gene symbol(s)
Thy1
Protein name(s)
OMP
Protein tag(s)
GFP, YFP
Datatype
neuron structure
Molecular Function (MF)
Biological Process (BP)
-
Cellular Component (CC)
-
Biological Imaging Method
-
XYZ Scale
XY: 1.59 micrometer/pixel, Z: 20.0 micrometer/slice, XY: 1.988 micrometer/pixel, Z: 13.0 micrometer/slice, XY: 1.59 micrometer/pixel, Z: 500.0 micrometer/slice, XY: 1.59 micrometer/pixel, Z: 25.0 micrometer/slice, XY: 1.446 micrometer/pixel, Z: 300.0 micrometer/slice, XY: 1.59 micrometer/pixel, Z: 200.0 micrometer/slice, XY: 1.242 micrometer/pixel, Z: 5.0 micrometer/slice, XY: 1.988 micrometer/pixel, Z: 5.0 micrometer/slice, XY: 1.382 micrometer/pixel, Z: 5.0 micrometer/slice, XY: 1.242 micrometer/pixel, Z: 4.0 micrometer/slice, XY: 1.59 micrometer/pixel, Z: 10.0 micrometer/slice, XY: 0.994 micrometer/pixel, Z: 5.0 micrometer/slice
T scale
-
Image Acquisition
Experiment type
Other
Microscope type
ConfocalMicroscope
Acquisition mode
LaserScanningConfocalMicroscopy
Contrast method
Fluorescence
Microscope model
Olympus FV1000 built on IX81 (confocal), Olympus FV1000MPE (two-photon)
Detector model
PMT, GaAsP
Objective model
Olympus XLPLN IMA-SP 25x/0.9, Olympus XLSLPLN25XSVMP 25x/0.9, Olympus XLPLN25XSVMP 25x/1.05 W, Olympus UMPLFLN 10x/0.3 W, Olympus UPLSAPO10X2 10x/0.4
Filter set
-
Related paper(s)

Meng-Tsen Ke, Satoshi Fujimoto, Takeshi Imai (2013) SeeDB: a simple and morphology-preserving optical clearing agent for neuronal circuit reconstruction., Nature neuroscience, Volume 16, Number 8, pp. 1154-61

Published in 2013 Aug (Electronic publication in June 23, 2013, midnight )

(Abstract) We report a water-based optical clearing agent, SeeDB, which clears fixed brain samples in a few days without quenching many types of fluorescent dyes, including fluorescent proteins and lipophilic neuronal tracers. Our method maintained a constant sample volume during the clearing procedure, an important factor for keeping cellular morphology intact, and facilitated the quantitative reconstruction of neuronal circuits. Combined with two-photon microscopy and an optimized objective lens, we were able to image the mouse brain from the dorsal to the ventral side. We used SeeDB to describe the near-complete wiring diagram of sister mitral cells associated with a common glomerulus in the mouse olfactory bulb. We found the diversity of dendrite wiring patterns among sister mitral cells, and our results provide an anatomical basis for non-redundant odor coding by these neurons. Our simple and efficient method is useful for imaging intact morphological architecture at large scales in both the adult and developing brains.
(MeSH Terms)
Contact
Takeshi Imai , RIKEN , Center for Developmental Biology , Laboratory for Sensory Circuit Formation
Contributors
Meng-Tsen Ke, Satoshi Fujimoto, Takeshi Imai

Dataset List of 25-Ke-SeeDB

#
Dataset ID
Kind
Size
4D View
SSBD:OMERO
Download BDML
Download Images
# 833
Datast ID Fig3A_Thy1-YFP-H
Dataset Kind Image data
Dataset Size 215.5 MB
4D view
SSBD:OMERO
Download BDML
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# 834
Datast ID Fig3B_Thy1-YFP-H
Dataset Kind Image data
Dataset Size 284.6 MB
4D view
SSBD:OMERO
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# 835
Datast ID Fig3C_Thy1-YFP-H_dv-2
Dataset Kind Image data
Dataset Size 566.8 MB
4D view
SSBD:OMERO
Download BDML
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# 836
Datast ID Fig3C_Thy1-YFP-H_dv-3
Dataset Kind Image data
Dataset Size 585.6 MB
4D view
SSBD:OMERO
Download BDML
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# 837
Datast ID Fig3D_Thy1-YFP-H
Dataset Kind Image data
Dataset Size 1.3 GB
4D view
SSBD:OMERO
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# 838
Datast ID Fig3E_Thy1-YFP-H
Dataset Kind Image data
Dataset Size 48.6 MB
4D view
SSBD:OMERO
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# 839
Datast ID Fig4_Thy1-YFP-H
Dataset Kind Image data
Dataset Size 358.2 MB
4D view
SSBD:OMERO
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# 840
Datast ID Fig5C_Thy1-YFP-H_injE
Dataset Kind Image data
Dataset Size 214.2 MB
4D view
SSBD:OMERO
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# 841
Datast ID Fig5C_Thy1-YFP-H_injG
Dataset Kind Image data
Dataset Size 198.1 MB
4D view
SSBD:OMERO
Download BDML
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# 842
Datast ID Fig5C_mitral_cell_1
Dataset Kind Image data
Dataset Size 198.1 MB
4D view
SSBD:OMERO
Download BDML
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# 843
Datast ID Fig5C_mitral_cell_2
Dataset Kind Image data
Dataset Size 121.5 MB
4D view
SSBD:OMERO
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# 844
Datast ID Fig5C_mitral_cell_3
Dataset Kind Image data
Dataset Size 214.2 MB
4D view
SSBD:OMERO
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# 845
Datast ID Fig5C_mitral_cell_4
Dataset Kind Image data
Dataset Size 137.6 MB
4D view
SSBD:OMERO
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# 846
Datast ID Fig5C_mitral_cell_5
Dataset Kind Image data
Dataset Size 532.6 MB
4D view
SSBD:OMERO
Download BDML
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# 847
Datast ID Fig6A_OMP-GFP
Dataset Kind Image data
Dataset Size 515.2 MB
4D view
SSBD:OMERO
Download BDML
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# 848
Datast ID FigS9_dorsal_face
Dataset Kind Image data
Dataset Size 380.2 MB
4D view
SSBD:OMERO
Download BDML
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# 849
Datast ID FigS10A_P72
Dataset Kind Image data
Dataset Size 752.5 MB
4D view
SSBD:OMERO
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# 850
Datast ID FigS10B_P72
Dataset Kind Image data
Dataset Size 2.4 GB
4D view
SSBD:OMERO
Download BDML
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# 851
Datast ID FigS11A_L_C
Dataset Kind Image data
Dataset Size 118.6 MB
4D view
SSBD:OMERO
Download BDML
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# 852
Datast ID FigS11A_L_L01
Dataset Kind Image data
Dataset Size 118.6 MB
4D view
SSBD:OMERO
Download BDML
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# 853
Datast ID FigS11A_L_L02
Dataset Kind Image data
Dataset Size 118.6 MB
4D view
SSBD:OMERO
Download BDML
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# 854
Datast ID FigS11A_L_L03
Dataset Kind Image data
Dataset Size 118.6 MB
4D view
SSBD:OMERO
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# 855
Datast ID FigS11A_L_L04
Dataset Kind Image data
Dataset Size 118.6 MB
4D view
SSBD:OMERO
Download BDML
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# 856
Datast ID FigS11A_L_L05
Dataset Kind Image data
Dataset Size 118.6 MB
4D view
SSBD:OMERO
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# 857
Datast ID FigS11A_L_L06
Dataset Kind Image data
Dataset Size 118.6 MB
4D view
SSBD:OMERO
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# 858
Datast ID FigS11A_L_L07
Dataset Kind Image data
Dataset Size 118.6 MB
4D view
SSBD:OMERO
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# 859
Datast ID FigS11A_L_L08
Dataset Kind Image data
Dataset Size 118.6 MB
4D view
SSBD:OMERO
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# 860
Datast ID FigS11A_L_L09
Dataset Kind Image data
Dataset Size 118.6 MB
4D view
SSBD:OMERO
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# 861
Datast ID FigS11A_L_L10
Dataset Kind Image data
Dataset Size 118.6 MB
4D view
SSBD:OMERO
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# 862
Datast ID FigS11A_L_L11
Dataset Kind Image data
Dataset Size 118.6 MB
4D view
SSBD:OMERO
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# 863
Datast ID FigS11A_L_L12
Dataset Kind Image data
Dataset Size 118.6 MB
4D view
SSBD:OMERO
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# 864
Datast ID FigS11A_L_L13
Dataset Kind Image data
Dataset Size 118.6 MB
4D view
SSBD:OMERO
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# 865
Datast ID FigS11A_L_L00
Dataset Kind Image data
Dataset Size 118.6 MB
4D view
SSBD:OMERO
Download BDML
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# 866
Datast ID FigS11A_R_C
Dataset Kind Image data
Dataset Size 127.7 MB
4D view
SSBD:OMERO
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# 867
Datast ID FigS11A_R_R01
Dataset Kind Image data
Dataset Size 127.7 MB
4D view
SSBD:OMERO
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# 868
Datast ID FigS11A_R_R02
Dataset Kind Image data
Dataset Size 127.7 MB
4D view
SSBD:OMERO
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# 869
Datast ID FigS11A_R_R03
Dataset Kind Image data
Dataset Size 127.7 MB
4D view
SSBD:OMERO
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# 870
Datast ID FigS11A_R_R04
Dataset Kind Image data
Dataset Size 127.8 MB
4D view
SSBD:OMERO
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# 871
Datast ID FigS11A_R_R05
Dataset Kind Image data
Dataset Size 127.8 MB
4D view
SSBD:OMERO
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# 872
Datast ID FigS11A_R_R06
Dataset Kind Image data
Dataset Size 127.7 MB
4D view
SSBD:OMERO
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# 873
Datast ID FigS11A_R_R07
Dataset Kind Image data
Dataset Size 127.8 MB
4D view
SSBD:OMERO
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# 874
Datast ID FigS11A_R_R08
Dataset Kind Image data
Dataset Size 127.7 MB
4D view
SSBD:OMERO
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# 875
Datast ID FigS11A_R_R09
Dataset Kind Image data
Dataset Size 127.7 MB
4D view
SSBD:OMERO
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# 876
Datast ID FigS11A_R_R10
Dataset Kind Image data
Dataset Size 127.7 MB
4D view
SSBD:OMERO
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# 877
Datast ID FigS11A_R_R11
Dataset Kind Image data
Dataset Size 127.7 MB
4D view
SSBD:OMERO
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# 878
Datast ID FigS11A_R_R12
Dataset Kind Image data
Dataset Size 127.7 MB
4D view
SSBD:OMERO
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# 879
Datast ID FigS11A_R_R13
Dataset Kind Image data
Dataset Size 127.7 MB
4D view
SSBD:OMERO
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# 880
Datast ID FigS11A_R_R14
Dataset Kind Image data
Dataset Size 127.7 MB
4D view
SSBD:OMERO
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# 881
Datast ID FigS11B_P21
Dataset Kind Image data
Dataset Size 1.9 GB
4D view
SSBD:OMERO
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# 882
Datast ID FigS11C_P21
Dataset Kind Image data
Dataset Size 616.1 MB
4D view
SSBD:OMERO
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# 883
Datast ID FigS12_P21
Dataset Kind Image data
Dataset Size 509.8 MB
4D view
SSBD:OMERO
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# 884
Datast ID FigS12_P7
Dataset Kind Image data
Dataset Size 1.7 GB
4D view
SSBD:OMERO
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