Summary of 95-Nojima-CellMorphology


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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

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#
Dataset ID
Kind
Size
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Thumbnail Thumbnail for dataset humanlung_d7
# 4265
Datast ID humanlung_d7
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset humanlung_d0_aSMA
# 4266
Datast ID humanlung_d0_aSMA
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset humanlung_d0_CD68
# 4267
Datast ID humanlung_d0_CD68
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset humanlung_d0_Cytokeratin
# 4268
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset humanlung_d4_aSMA
# 4269
Datast ID humanlung_d4_aSMA
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset humanlung_d4_CD68
# 4270
Datast ID humanlung_d4_CD68
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset humanlung_d4_Cytokeratin
# 4271
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset humanlung_d7_aSMA
# 4272
Datast ID humanlung_d7_aSMA
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset humanlung_d7_CD68
# 4273
Datast ID humanlung_d7_CD68
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset humanlung_d7_Cytokeratin
# 4274
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset humanspleen_d0
# 4275
Datast ID humanspleen_d0
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset humanspleen_d2
# 4276
Datast ID humanspleen_d2
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset humanspleen_d3
# 4277
Datast ID humanspleen_d3
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset humanspleen_d5
# 4278
Datast ID humanspleen_d5
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset humanspleen_d8
# 4279
Datast ID humanspleen_d8
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset humanspleen_d16
# 4280
Datast ID humanspleen_d16
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset mouseheart_d0
# 4281
Datast ID mouseheart_d0
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset mouseheart_d2
# 4282
Datast ID mouseheart_d2
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset mouseheart_d3
# 4283
Datast ID mouseheart_d3
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset mouseheart_d5
# 4284
Datast ID mouseheart_d5
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset mouseheart_d8
# 4285
Datast ID mouseheart_d8
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset mouseheart_d16
# 4286
Datast ID mouseheart_d16
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset mouseintestine_d0
# 4287
Datast ID mouseintestine_d0
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset mouseintestine_d2
# 4288
Datast ID mouseintestine_d2
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset mouseintestine_d3
# 4289
Datast ID mouseintestine_d3
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset mouseintestine_d5
# 4290
Datast ID mouseintestine_d5
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset mouseintestine_d8
# 4291
Datast ID mouseintestine_d8
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset mouseintestine_d16
# 4292
Datast ID mouseintestine_d16
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset mousekidney_d0
# 4293
Datast ID mousekidney_d0
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset mousekidney_d2
# 4294
Datast ID mousekidney_d2
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset mousekidney_d3
# 4295
Datast ID mousekidney_d3
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset mousekidney_d5
# 4296
Datast ID mousekidney_d5
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset mousekidney_d8
# 4297
Datast ID mousekidney_d8
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset mousekidney_d16
# 4298
Datast ID mousekidney_d16
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset mouseliver_d0
# 4299
Datast ID mouseliver_d0
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset mouseliver_d2
# 4300
Datast ID mouseliver_d2
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset mouseliver_d3
# 4301
Datast ID mouseliver_d3
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset mouseliver_d5
# 4302
Datast ID mouseliver_d5
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset mouseliver_d8
# 4303
Datast ID mouseliver_d8
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset mouseliver_d16
# 4304
Datast ID mouseliver_d16
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset mouseLN_d0
# 4305
Datast ID mouseLN_d0
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset mouseLN_d2
# 4306
Datast ID mouseLN_d2
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset mouseLN_d3
# 4307
Datast ID mouseLN_d3
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset mouseLN_d4
# 4308
Datast ID mouseLN_d4
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset mouseLN_d6
# 4309
Datast ID mouseLN_d6
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset mouseLN_d7
# 4310
Datast ID mouseLN_d7
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset mouselung_d0
# 4311
Datast ID mouselung_d0
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset mouselung_d2
# 4312
Datast ID mouselung_d2
Dataset Kind Image data
Dataset Size 5.5 MB
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SSBD:OMERO
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Thumbnail Thumbnail for dataset mouselung_d3
# 4313
Datast ID mouselung_d3
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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Thumbnail Thumbnail for dataset mouselung_d4
# 4314
Datast ID mouselung_d4
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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