Summary of 95-Nojima-CellMorphology

SSBD:database
SSBD:database URL
Title
HE staining images of human and mouse organs with CUBIC
Description
-
Relase 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)
M. musculus, H. sapiens

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

#
Dataset ID
Kind
Size
4D View
SSBD:OMERO
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# 4215
Datast ID humanbrain_d0
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4216
Datast ID humanbrain_d2
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4217
Datast ID humanbrain_d3
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4218
Datast ID humanbrain_d5
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4219
Datast ID humanbrain_d8
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4220
Datast ID humanbrain_d16
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4221
Datast ID humanheart_d0
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4222
Datast ID humanheart_d2
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4223
Datast ID humanheart_d3
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4224
Datast ID humanheart_d5
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4225
Datast ID humanheart_d8
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4226
Datast ID humanheart_d16
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4227
Datast ID humanintestine_d0
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4228
Datast ID humanintestine_d2
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4229
Datast ID humanintestine_d3
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4230
Datast ID humanintestine_d5
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4231
Datast ID humanintestine_d8
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4232
Datast ID humanintestine_d16
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4233
Datast ID humankidney_d0
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4234
Datast ID humankidney_d2
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4235
Datast ID humankidney_d3
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4236
Datast ID humankidney_d5
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4237
Datast ID humankidney_d8
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4238
Datast ID humankidney_d16
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4239
Datast ID humanliver_d0
Dataset Kind Image data
Dataset Size 1.5 MB
4D view
SSBD:OMERO
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# 4240
Datast ID humanliver_d2
Dataset Kind Image data
Dataset Size 1.5 MB
4D view
SSBD:OMERO
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# 4241
Datast ID humanliver_d3
Dataset Kind Image data
Dataset Size 1.5 MB
4D view
SSBD:OMERO
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# 4242
Datast ID humanliver_d5
Dataset Kind Image data
Dataset Size 1.5 MB
4D view
SSBD:OMERO
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# 4243
Datast ID humanliver_d8
Dataset Kind Image data
Dataset Size 1.5 MB
4D view
SSBD:OMERO
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# 4244
Datast ID humanliver_d16
Dataset Kind Image data
Dataset Size 1.5 MB
4D view
SSBD:OMERO
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# 4245
Datast ID humanLN_CD3_d0
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4246
Datast ID humanLN_CD3_d4
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4247
Datast ID humanLN_CD3_d7
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4248
Datast ID humanLN_CD68_d0
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4249
Datast ID humanLN_CD68_d4
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4250
Datast ID humanLN_CD68_d7
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4251
Datast ID humanLN_CD79a_d0
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4252
Datast ID humanLN_CD79a_d4
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4253
Datast ID humanLN_CD79a_d7
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4254
Datast ID humanLN_d0
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4255
Datast ID humanLN_d2
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4256
Datast ID humanLN_d3
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4257
Datast ID humanLN_d4
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4258
Datast ID humanLN_d6
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4259
Datast ID humanLN_d7
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4260
Datast ID humanlung_d0
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4261
Datast ID humanlung_d2
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4262
Datast ID humanlung_d3
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4263
Datast ID humanlung_d4
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4264
Datast ID humanlung_d6
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4265
Datast ID humanlung_d7
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4266
Datast ID humanlung_d0_aSMA
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4267
Datast ID humanlung_d0_CD68
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4268
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4269
Datast ID humanlung_d4_aSMA
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4270
Datast ID humanlung_d4_CD68
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4271
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4272
Datast ID humanlung_d7_aSMA
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4273
Datast ID humanlung_d7_CD68
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4274
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4275
Datast ID humanspleen_d0
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4276
Datast ID humanspleen_d2
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4277
Datast ID humanspleen_d3
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4278
Datast ID humanspleen_d5
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4279
Datast ID humanspleen_d8
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4280
Datast ID humanspleen_d16
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4281
Datast ID mouseheart_d0
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4282
Datast ID mouseheart_d2
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4283
Datast ID mouseheart_d3
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4284
Datast ID mouseheart_d5
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4285
Datast ID mouseheart_d8
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4286
Datast ID mouseheart_d16
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4287
Datast ID mouseintestine_d0
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4288
Datast ID mouseintestine_d2
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4289
Datast ID mouseintestine_d3
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4290
Datast ID mouseintestine_d5
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4291
Datast ID mouseintestine_d8
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4292
Datast ID mouseintestine_d16
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4293
Datast ID mousekidney_d0
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4294
Datast ID mousekidney_d2
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4295
Datast ID mousekidney_d3
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4296
Datast ID mousekidney_d5
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4297
Datast ID mousekidney_d8
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4298
Datast ID mousekidney_d16
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4299
Datast ID mouseliver_d0
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4300
Datast ID mouseliver_d2
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4301
Datast ID mouseliver_d3
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4302
Datast ID mouseliver_d5
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4303
Datast ID mouseliver_d8
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4304
Datast ID mouseliver_d16
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4305
Datast ID mouseLN_d0
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4306
Datast ID mouseLN_d2
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4307
Datast ID mouseLN_d3
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4308
Datast ID mouseLN_d4
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4309
Datast ID mouseLN_d6
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4310
Datast ID mouseLN_d7
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4311
Datast ID mouselung_d0
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4312
Datast ID mouselung_d2
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4313
Datast ID mouselung_d3
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4314
Datast ID mouselung_d4
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4315
Datast ID mouselung_d6
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4316
Datast ID mouselung_d7
Dataset Kind Image data
Dataset Size 5.5 MB
4D view
SSBD:OMERO
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# 4317
Datast ID mousespleen_d0
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4318
Datast ID mousespleen_d2
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4319
Datast ID mousespleen_d3
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4320
Datast ID mousespleen_d5
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4321
Datast ID mousespleen_d8
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4322
Datast ID mousespleen_d16
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4323
Datast ID muosebrain_d0
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4324
Datast ID muosebrain_d2
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4325
Datast ID muosebrain_d3
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4326
Datast ID muosebrain_d5
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4327
Datast ID muosebrain_d8
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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# 4328
Datast ID muosebrain_d16
Dataset Kind Image data
Dataset Size 5.6 MB
4D view
SSBD:OMERO
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