Summary of 49-Susaki-MouseBrainCUBIC

SSBD:database
SSBD:database URL
Title
-
Description
-
Relase date
2017-10-03
Updated date
2018-11-15
License
CC BY
Kind
Image data based on Experiment
Number of Datasets
1 ( Image datasets: 1, Quantitative data datasets: 0 )
Size of Datasets
5.3 GB ( Image datasets: 5.3 GB, Quantitative data datasets: 0 bytes )

Organism(s)
M. musculus
Gene symbol(s)
Arc, Thy1
Protein tag(s)
YFP, dVenus

Datatype
organ structure
Molecular Function (MF)
Biological Process (BP)
-
Cellular Component (CC)
-
Biological Imaging Method
-
XYZ Scale
XY: 6.45 micrometer/pixel, Z: 10 micrometer/frame
T scale
-

Image Acquisition
Experiment type
Other
Microscope type
ConfocalMicroscope
Acquisition mode
LaserScanningConfocalMicroscopy
Contrast method
Fluorescence
Microscope model
LaVision Bio Tec Ultramicroscope + Olympus MVX-ZB10
Detector model
Andor sCMOS CCD camera Neo 5.5
Objective model
Olympus MVPLAPO 0.63x/0.15
Filter set
Ultramicroscope filter wheel unit

Related paper(s)

Etsuo A Susaki, Kazuki Tainaka, Dimitri Perrin, Hiroko Yukinaga, Akihiro Kuno, Hiroki R Ueda (2015) Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging., Nature protocols, Volume 10, Number 11, pp. 1709-27

Published in 2015 Nov (Electronic publication in Oct. 8, 2015, midnight )

(Abstract) Here we describe a protocol for advanced CUBIC (Clear, Unobstructed Brain/Body Imaging Cocktails and Computational analysis). The CUBIC protocol enables simple and efficient organ clearing, rapid imaging by light-sheet microscopy and quantitative imaging analysis of multiple samples. The organ or body is cleared by immersion for 1-14 d, with the exact time required dependent on the sample type and the experimental purposes. A single imaging set can be completed in 30-60 min. Image processing and analysis can take <1 d, but it is dependent on the number of samples in the data set. The CUBIC clearing protocol can process multiple samples simultaneously. We previously used CUBIC to image whole-brain neural activities at single-cell resolution using Arc-dVenus transgenic (Tg) mice. CUBIC informatics calculated the Venus signal subtraction, comparing different brains at a whole-organ scale. These protocols provide a platform for organism-level systems biology by comprehensively detecting cells in a whole organ or body.
(MeSH Terms)

Contact
Hiroki R Ueda , RIKEN , Quantitative Biology Center , Laboratory for Synthetic Biology
Contributors
Etsuo A Susaki, Kazuki Tainaka, Dimitri Perrin, Hiroko Yukinaga, Akihiro Kuno, Hiroki R Ueda


Dataset List of 49-Susaki-MouseBrainCUBIC

#
Dataset ID
Kind
Size
4D View
SSBD:OMERO
Download BDML
Download Images
# 1306
Dataset Kind Image data
Dataset Size 5.3 GB
4D view
SSBD:OMERO
Download BDML
Download Image data