Summary of 11-Toyoshima-NeuAct

SSBD:database
SSBD:database URL

SSBD:repository
SSBD:repository URL

Title
Quantitative information about neuronal nuclei in C. elegans adult
Description
-
Relase date
2016-05-20
Updated date
2018-11-15
License
CC BY-NC-SA
Kind
Quantitative data, Image data based on Experiment
Number of Datasets
28 ( Image datasets: 14, Quantitative data datasets: 14 )
Size of Datasets
20.5 GB ( Image datasets: 20.4 GB, Quantitative data datasets: 67.8 MB )

Organism(s)
C. elegans
Gene symbol(s)
NA
Protein name(s)
NA

Datatype
neuronal nuclear dynamics
Molecular Function (MF)
Biological Process (BP)
-
Cellular Component (CC)
nucleus
Biological Imaging Method
-
XYZ Scale
XY: 0.24 micrometer/pixel, Z: 0.252 micrometer/slice, XY: 0.25 micrometer/pixel, Z: 0 micrometer/slice, XY: 0.33 micrometer/pixel, Z: 1.4 micrometer/slice
T scale
0.21 second for each time interval, 0 second for each time interval, 0.545 second for each time interval

Image Acquisition
Experiment type
-
Microscope type
-
Acquisition mode
-
Contrast method
-
Microscope model
-
Detector model
-
Objective model
-
Filter set
-

Related paper(s)

Yu Toyoshima, Terumasa Tokunaga, Osamu Hirose, Manami Kanamori, Takayuki Teramoto, Moon Sun Jang, Sayuri Kuge, Takeshi Ishihara, Ryo Yoshida, Yuichi Iino (2016) Accurate Automatic Detection of Densely Distributed Cell Nuclei in 3D Space., PLoS computational biology, Volume 12, Number 6, pp. e1004970

Published in 2016 Jun (Electronic publication in June 6, 2016, midnight )

(Abstract) To measure the activity of neurons using whole-brain activity imaging, precise detection of each neuron or its nucleus is required. In the head region of the nematode C. elegans, the neuronal cell bodies are distributed densely in three-dimensional (3D) space. However, no existing computational methods of image analysis can separate them with sufficient accuracy. Here we propose a highly accurate segmentation method based on the curvatures of the iso-intensity surfaces. To obtain accurate positions of nuclei, we also developed a new procedure for least squares fitting with a Gaussian mixture model. Combining these methods enables accurate detection of densely distributed cell nuclei in a 3D space. The proposed method was implemented as a graphical user interface program that allows visualization and correction of the results of automatic detection. Additionally, the proposed method was applied to time-lapse 3D calcium imaging data, and most of the nuclei in the images were successfully tracked and measured.
(MeSH Terms)

Contact
Yu Toyoshima , The University of Tokyo , Department of Biological Sciences , Iino Laboratory
Contributors
Yu Toyoshima, Terumasa Tokunaga, Osamu Hirose, Manami Kanamori, Takayuki Teramoto, Moon Sun Jang, Sayuri Kuge, Takeshi Ishihara, Ryo Yoshida, Yuichi Iino


Dataset List of 11-Toyoshima-NeuAct

#
Dataset ID
Kind
Size
4D View
SSBD:OMERO
Download BDML
Download Images
# 508
Dataset Kind Image data
Dataset Size 244.3 MB
4D view
SSBD:OMERO
Download BDML
Download Image data

# 509
Dataset Kind Quantitative data
Dataset Size 113.2 KB
4D view
SSBD:OMERO
Download BDML
Download Image data

# 510
Dataset Kind Image data
Dataset Size 247.9 MB
4D view
SSBD:OMERO
Download BDML
Download Image data

# 511
Dataset Kind Quantitative data
Dataset Size 110.6 KB
4D view
SSBD:OMERO
Download BDML
Download Image data

# 512
Dataset Kind Image data
Dataset Size 225.6 MB
4D view
SSBD:OMERO
Download BDML
Download Image data

# 513
Dataset Kind Quantitative data
Dataset Size 112.7 KB
4D view
SSBD:OMERO
Download BDML
Download Image data

# 514
Dataset Kind Image data
Dataset Size 277.9 MB
4D view
SSBD:OMERO
Download BDML
Download Image data

# 515
Dataset Kind Quantitative data
Dataset Size 116.5 KB
4D view
SSBD:OMERO
Download BDML
Download Image data

# 516
Dataset Kind Image data
Dataset Size 261.1 MB
4D view
SSBD:OMERO
Download BDML
Download Image data

# 517
Dataset Kind Quantitative data
Dataset Size 112.7 KB
4D view
SSBD:OMERO
Download BDML
Download Image data

# 518
Dataset Kind Image data
Dataset Size 266.2 MB
4D view
SSBD:OMERO
Download BDML
Download Image data

# 519
Dataset Kind Quantitative data
Dataset Size 113.8 KB
4D view
SSBD:OMERO
Download BDML
Download Image data

# 520
Dataset Kind Image data
Dataset Size 284.1 MB
4D view
SSBD:OMERO
Download BDML
Download Image data

# 521
Dataset Kind Quantitative data
Dataset Size 112.7 KB
4D view
SSBD:OMERO
Download BDML
Download Image data

# 522
Dataset Kind Image data
Dataset Size 253.4 MB
4D view
SSBD:OMERO
Download BDML
Download Image data

# 523
Dataset Kind Quantitative data
Dataset Size 110.6 KB
4D view
SSBD:OMERO
Download BDML
Download Image data

# 524
Dataset Kind Image data
Dataset Size 253.0 MB
4D view
SSBD:OMERO
Download BDML
Download Image data

# 525
Dataset Kind Quantitative data
Dataset Size 107.9 KB
4D view
SSBD:OMERO
Download BDML
Download Image data

# 526
Dataset Kind Image data
Dataset Size 250.5 MB
4D view
SSBD:OMERO
Download BDML
Download Image data

# 527
Dataset Kind Quantitative data
Dataset Size 111.6 KB
4D view
SSBD:OMERO
Download BDML
Download Image data

# 528
Dataset Kind Image data
Dataset Size 270.3 MB
4D view
SSBD:OMERO
Download BDML
Download Image data

# 529
Dataset Kind Quantitative data
Dataset Size 114.3 KB
4D view
SSBD:OMERO
Download BDML
Download Image data

# 530
Dataset Kind Image data
Dataset Size 235.9 MB
4D view
SSBD:OMERO
Download BDML
Download Image data

# 531
Dataset Kind Quantitative data
Dataset Size 112.2 KB
4D view
SSBD:OMERO
Download BDML
Download Image data

# 532
Dataset Kind Image data
Dataset Size 17.3 GB
4D view
SSBD:OMERO
Download BDML
Download Image data

# 533
Dataset Kind Quantitative data
Dataset Size 63.6 MB
4D view
SSBD:OMERO
Download BDML
Download Image data

# 534
Datast ID tax4_7_t1
Dataset Kind Image data
Dataset Size 120.5 MB
4D view
SSBD:OMERO
Download BDML
Download Image data

# 535
Datast ID tax4_7_t1
Dataset Kind Quantitative data
Dataset Size 2.9 MB
4D view
SSBD:OMERO
Download BDML
Download Image data