Summary of 95-Nojima-CellMorphology


SSBD:database
SSBD:database URL

SSBD:repository
SSBD:repository URL

Title
HE staining images of human and mouse organs with CUBIC
Description
-
Release date
2018-11-14
Updated date
-
License
CC BY
Kind
Image data based on Experiment
Number of Datasets
114 ( Image datasets: 114, Quantitative data datasets: 0 )
Size of Datasets
608.2 MB ( Image datasets: 608.2 MB, Quantitative data datasets: 0 bytes )

Organism(s)
Homo sapiens, Mus musculus

Datatype
cell morphology
Molecular Function (MF)
Biological Process (BP)
lung growth, lymph node development
Cellular Component (CC)
-
Biological Imaging Method
-
XYZ Scale
XY: 0.55 micrometer/pixel, Z: NA
T scale
-

Image Acquisition
Experiment type
Immunocytochemistry
Microscope type
ConfocalMicroscope
Acquisition mode
BrightField
Contrast method
Brightfield
Microscope model
Carl-Zeiss Zeiss LSM710
Detector model
-
Objective model
-
Filter set
-

Related paper(s)

Satoshi Nojima, Etsuo A Susaki, Kyotaro Yoshida, Hiroyoshi Takemoto, Naoto Tsujimura, Shohei Iijima, Ko Takachi, Yujiro Nakahara, Shinichiro Tahara, Kenji Ohshima, Masako Kurashige, Yumiko Hori, Naoki Wada, Jun-Ichiro Ikeda, Atsushi Kumanogoh, Eiichi Morii, Hiroki R Ueda (2017) CUBIC pathology: three-dimensional imaging for pathological diagnosis., Scientific reports, Volume 7, Number 1, pp. 9269

Published in 2017 Aug 24 (Electronic publication in Aug. 24, 2017, midnight )

(Abstract) The examination of hematoxylin and eosin (H&E)-stained tissues on glass slides by conventional light microscopy is the foundation for histopathological diagnosis. However, this conventional method has some limitations in x-y axes due to its relatively narrow range of observation area and in z-axis due to its two-dimensionality. In this study, we applied a CUBIC pipeline, which is the most powerful tissue-clearing and three-dimensional (3D)-imaging technique, to clinical pathology. CUBIC was applicable to 3D imaging of both normal and abnormal patient-derived, human lung and lymph node tissues. Notably, the combination of deparaffinization and CUBIC enabled 3D imaging of specimens derived from paraffin-embedded tissue blocks, allowing quantitative evaluation of nuclear and structural atypia of an archival malignant lymphoma tissue. Furthermore, to examine whether CUBIC can be applied to practical use in pathological diagnosis, we performed a histopathological screening of a lymph node metastasis based on CUBIC, which successfully improved the sensitivity in detecting minor metastatic carcinoma nodules in lymph nodes. Collectively, our results indicate that CUBIC significantly contributes to retrospective and prospective clinicopathological diagnosis, which might lead to the establishment of a novel field of medical science based on 3D histopathology.
(MeSH Terms)

Contact
Hiroki R. Ueda , RIKEN , Center for Biosystems Dynamics Research , Laboratory for Synthetic Biology
Contributors
Satoshi Nojima, Etsuo A. Susaki, Kyotaro Yoshida, Hiroyoshi Takemoto, Naoto Tsujimura, Shohei Iijima, Ko Takachi, Yujiro Nakahara, Shinichiro Tahara, Kenji Ohshima, Masako Kurashige, Yumiko Hori, Naoki Wada, Jun-ichiro Ikeda, Atsushi Kumanogoh, Eiichi Morii, Hiroki R. Ueda

Dataset List of 95-Nojima-CellMorphology

Thumbnail
#
Dataset ID
Kind
Size
4D View
SSBD:OMERO
Download BDML
Download Images
Thumbnail Thumbnail for dataset mouselung_d6
# 4315
Datast ID mouselung_d6
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
Download BDML
Download Image data

Thumbnail Thumbnail for dataset mouselung_d7
# 4316
Datast ID mouselung_d7
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
Download BDML
Download Image data

Thumbnail Thumbnail for dataset mousespleen_d0
# 4317
Datast ID mousespleen_d0
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
Download BDML
Download Image data

Thumbnail Thumbnail for dataset mousespleen_d2
# 4318
Datast ID mousespleen_d2
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
Download BDML
Download Image data

Thumbnail Thumbnail for dataset mousespleen_d3
# 4319
Datast ID mousespleen_d3
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
Download BDML
Download Image data

Thumbnail Thumbnail for dataset mousespleen_d5
# 4320
Datast ID mousespleen_d5
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
Download BDML
Download Image data

Thumbnail Thumbnail for dataset mousespleen_d8
# 4321
Datast ID mousespleen_d8
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
Download BDML
Download Image data

Thumbnail Thumbnail for dataset mousespleen_d16
# 4322
Datast ID mousespleen_d16
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
Download BDML
Download Image data

Thumbnail Thumbnail for dataset muosebrain_d0
# 4323
Datast ID muosebrain_d0
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
Download BDML
Download Image data

Thumbnail Thumbnail for dataset muosebrain_d2
# 4324
Datast ID muosebrain_d2
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
Download BDML
Download Image data

Thumbnail Thumbnail for dataset muosebrain_d3
# 4325
Datast ID muosebrain_d3
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
Download BDML
Download Image data

Thumbnail Thumbnail for dataset muosebrain_d5
# 4326
Datast ID muosebrain_d5
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
Download BDML
Download Image data

Thumbnail Thumbnail for dataset muosebrain_d8
# 4327
Datast ID muosebrain_d8
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
Download BDML
Download Image data

Thumbnail Thumbnail for dataset muosebrain_d16
# 4328
Datast ID muosebrain_d16
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
Download BDML
Download Image data