Summary of 296-Kawabata-MouseBrainShape

SSBD:database
SSBD:database URL
DOI
Title
Image processing and manual annotation data of mouse brains with neurogenic-tagged neurons from NeuroGT database
Description
Segmentation results of brain contours and tagged neurons for 168 imaging data sets provided from NeuroGT database and manual annotation data of anatomical regions (isocortex, olfactory area, hippocampal formation, cerebral nuclei, interbrain, midbrain, hindbrain, and cerebellum) for images (131 images for the G2AN_TM11.5_L dataset and 10 images each for the other datasets) targeted mouse brains for evaluation
Relase date
2023-05-09
Updated date
2023-05-29
Errata
2023/05/29 All BDML/BD5 data was updated cause of some format error in BD5
License
CC BY
Kind
Quantitative data based on Experiment
Number of Datasets
168 ( Image datasets: 0, Quantitative data datasets: 168 )
Size of Datasets
100.2 GB ( Image datasets: 0 bytes, Quantitative data datasets: 100.2 GB )

Organism(s)
Mus musculus
Strain(s)
C57BL/6 Neurod4^{CreER}(D4A); Tau^{mGFP-nLacZ}, C57BL/6 neuroG2^{CreER}(G2A); Tau^{mGFP-nLacZ}, C57BL/6 Neurod1^{CreER}(D1B); Tau^{mGFP-nLacZ}, C57BL/6 Neurog1^{CreER}(G1C); Tau^{mGFP-nLacZ}

Datatype
-
Molecular Function (MF)
Biological Process (BP)
nervous system development
Cellular Component (CC)
neuron projection, plasma membrane
Biological Imaging Method
chemically fixed tissue, horseradish peroxidase, cryostat-sectioned tissue, bright-field microscopy
X scale
1.0 micrometer/pixel
Y scale
1.0 micrometer/pixel
Z scale
20 micrometer/slice
T scale
-

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

Related paper(s)

Kawabata, Hiroto, Shimojo, Yuki, Hirata, Tatsumi, Tohsato, Yukako (2023) Large-scale Image Processing and Three-Dimensional Reconstruction of Mouse Brains with Neurogenic-Tagged Neurons, 1-7

Published in Dec. 19, 2023

(Abstract) The NeuroGT (neurogenic tagging) database provides images of whole-brain sections of mice in which neurons that differentiated at a similar time have been genetically tagged. The images of brain sections are displayed in order from the anterior to the posterior end on a web-browser, and the regions containing tagged neurons can be visually confirmed. However, it has been difficult to grasp their location in three-dimensional (3D) space. As a first step toward quantitative analysis of neuronal location, we automatically detected regions of mouse brains containing tagged neurons by using image processing and integrated that information into 3D space. We confirmed that the proposed methods detected brain regions with an average precision of 88% and average recall of 99%. We achieved visualization of 3D reconstructed brain shapes and distribution of tagged neurons in the regions of the brain.

Contact
Yukako Tohsato , Ritsumeikan University , Faculty of Information Science and Engineering , Laboratory of compubational biology
Contributors
Hiroto Kawabata, Yuki Shimojo, Tatsumi Hirata, Yukako Tohsato


Dataset List of 296-Kawabata-MouseBrainShape

#
Dataset ID
Kind
Size
4D View
SSBD:OMERO
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# 10497
Dataset Kind Quantitative data
Dataset Size 5.6 GB
4D view
SSBD:OMERO
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# 10498
Dataset Kind Quantitative data
Dataset Size 95.1 MB
4D view
SSBD:OMERO
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# 10499
Dataset Kind Quantitative data
Dataset Size 2.5 GB
4D view
SSBD:OMERO
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# 10500
Dataset Kind Quantitative data
Dataset Size 89.5 MB
4D view
SSBD:OMERO
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# 10501
Dataset Kind Quantitative data
Dataset Size 3.9 GB
4D view
SSBD:OMERO
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# 10502
Dataset Kind Quantitative data
Dataset Size 137.2 MB
4D view
SSBD:OMERO
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# 10503
Dataset Kind Quantitative data
Dataset Size 5.0 GB
4D view
SSBD:OMERO
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# 10504
Dataset Kind Quantitative data
Dataset Size 124.0 MB
4D view
SSBD:OMERO
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# 10505
Dataset Kind Quantitative data
Dataset Size 7.7 GB
4D view
SSBD:OMERO
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# 10506
Dataset Kind Quantitative data
Dataset Size 98.8 MB
4D view
SSBD:OMERO
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# 10507
Dataset Kind Quantitative data
Dataset Size 4.8 GB
4D view
SSBD:OMERO
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# 10508
Dataset Kind Quantitative data
Dataset Size 99.0 MB
4D view
SSBD:OMERO
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# 10509
Dataset Kind Quantitative data
Dataset Size 406.1 MB
4D view
SSBD:OMERO
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# 10510
Dataset Kind Quantitative data
Dataset Size 89.2 MB
4D view
SSBD:OMERO
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# 10511
Dataset Kind Quantitative data
Dataset Size 4.1 GB
4D view
SSBD:OMERO
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# 10512
Dataset Kind Quantitative data
Dataset Size 124.5 MB
4D view
SSBD:OMERO
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# 10513
Dataset Kind Quantitative data
Dataset Size 13.4 GB
4D view
SSBD:OMERO
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# 10514
Dataset Kind Quantitative data
Dataset Size 142.6 MB
4D view
SSBD:OMERO
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# 10515
Dataset Kind Quantitative data
Dataset Size 2.6 GB
4D view
SSBD:OMERO
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# 10516
Dataset Kind Quantitative data
Dataset Size 95.4 MB
4D view
SSBD:OMERO
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# 10517
Dataset Kind Quantitative data
Dataset Size 248.3 MB
4D view
SSBD:OMERO
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# 10518
Dataset Kind Quantitative data
Dataset Size 2.0 GB
4D view
SSBD:OMERO
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# 10519
Dataset Kind Quantitative data
Dataset Size 1.5 GB
4D view
SSBD:OMERO
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# 10520
Dataset Kind Quantitative data
Dataset Size 217.3 MB
4D view
SSBD:OMERO
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# 10521
Dataset Kind Quantitative data
Dataset Size 2.1 GB
4D view
SSBD:OMERO
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# 10522
Dataset Kind Quantitative data
Dataset Size 305.7 MB
4D view
SSBD:OMERO
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# 10523
Dataset Kind Quantitative data
Dataset Size 1.2 GB
4D view
SSBD:OMERO
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# 10524
Dataset Kind Quantitative data
Dataset Size 467.5 MB
4D view
SSBD:OMERO
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# 10525
Dataset Kind Quantitative data
Dataset Size 901.8 MB
4D view
SSBD:OMERO
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# 10526
Dataset Kind Quantitative data
Dataset Size 358.2 MB
4D view
SSBD:OMERO
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# 10527
Dataset Kind Quantitative data
Dataset Size 388.8 MB
4D view
SSBD:OMERO
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# 10528
Dataset Kind Quantitative data
Dataset Size 275.3 MB
4D view
SSBD:OMERO
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# 10529
Dataset Kind Quantitative data
Dataset Size 195.2 MB
4D view
SSBD:OMERO
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# 10530
Dataset Kind Quantitative data
Dataset Size 108.2 MB
4D view
SSBD:OMERO
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# 10531
Dataset Kind Quantitative data
Dataset Size 295.5 MB
4D view
SSBD:OMERO
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# 10532
Dataset Kind Quantitative data
Dataset Size 311.1 MB
4D view
SSBD:OMERO
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# 10533
Dataset Kind Quantitative data
Dataset Size 216.8 MB
4D view
SSBD:OMERO
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# 10534
Dataset Kind Quantitative data
Dataset Size 302.1 MB
4D view
SSBD:OMERO
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# 10535
Dataset Kind Quantitative data
Dataset Size 89.7 MB
4D view
SSBD:OMERO
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# 10536
Dataset Kind Quantitative data
Dataset Size 85.2 MB
4D view
SSBD:OMERO
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# 10537
Dataset Kind Quantitative data
Dataset Size 157.8 MB
4D view
SSBD:OMERO
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# 10538
Dataset Kind Quantitative data
Dataset Size 681.8 MB
4D view
SSBD:OMERO
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# 10539
Dataset Kind Quantitative data
Dataset Size 378.4 MB
4D view
SSBD:OMERO
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# 10540
Dataset Kind Quantitative data
Dataset Size 127.7 MB
4D view
SSBD:OMERO
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# 10541
Dataset Kind Quantitative data
Dataset Size 1.6 GB
4D view
SSBD:OMERO
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# 10542
Dataset Kind Quantitative data
Dataset Size 158.0 MB
4D view
SSBD:OMERO
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# 10543
Dataset Kind Quantitative data
Dataset Size 194.7 MB
4D view
SSBD:OMERO
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# 10544
Dataset Kind Quantitative data
Dataset Size 182.1 MB
4D view
SSBD:OMERO
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# 10545
Dataset Kind Quantitative data
Dataset Size 325.4 MB
4D view
SSBD:OMERO
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# 10546
Dataset Kind Quantitative data
Dataset Size 110.9 MB
4D view
SSBD:OMERO
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# 10547
Dataset Kind Quantitative data
Dataset Size 306.0 MB
4D view
SSBD:OMERO
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# 10548
Dataset Kind Quantitative data
Dataset Size 138.6 MB
4D view
SSBD:OMERO
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# 10549
Dataset Kind Quantitative data
Dataset Size 98.2 MB
4D view
SSBD:OMERO
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# 10550
Dataset Kind Quantitative data
Dataset Size 95.2 MB
4D view
SSBD:OMERO
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# 10551
Dataset Kind Quantitative data
Dataset Size 285.7 MB
4D view
SSBD:OMERO
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# 10552
Dataset Kind Quantitative data
Dataset Size 303.5 MB
4D view
SSBD:OMERO
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# 10553
Dataset Kind Quantitative data
Dataset Size 188.5 MB
4D view
SSBD:OMERO
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# 10554
Dataset Kind Quantitative data
Dataset Size 138.6 MB
4D view
SSBD:OMERO
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# 10555
Dataset Kind Quantitative data
Dataset Size 189.9 MB
4D view
SSBD:OMERO
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# 10556
Dataset Kind Quantitative data
Dataset Size 118.1 MB
4D view
SSBD:OMERO
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# 10557
Dataset Kind Quantitative data
Dataset Size 386.7 MB
4D view
SSBD:OMERO
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# 10558
Dataset Kind Quantitative data
Dataset Size 170.2 MB
4D view
SSBD:OMERO
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# 10559
Dataset Kind Quantitative data
Dataset Size 4.3 GB
4D view
SSBD:OMERO
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# 10560
Dataset Kind Quantitative data
Dataset Size 305.8 MB
4D view
SSBD:OMERO
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# 10561
Dataset Kind Quantitative data
Dataset Size 3.0 GB
4D view
SSBD:OMERO
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# 10562
Dataset Kind Quantitative data
Dataset Size 194.6 MB
4D view
SSBD:OMERO
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# 10563
Dataset Kind Quantitative data
Dataset Size 2.0 GB
4D view
SSBD:OMERO
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# 10564
Dataset Kind Quantitative data
Dataset Size 750.7 MB
4D view
SSBD:OMERO
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# 10565
Dataset Kind Quantitative data
Dataset Size 2.9 GB
4D view
SSBD:OMERO
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# 10566
Dataset Kind Quantitative data
Dataset Size 627.0 MB
4D view
SSBD:OMERO
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# 10567
Dataset Kind Quantitative data
Dataset Size 2.2 GB
4D view
SSBD:OMERO
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# 10568
Dataset Kind Quantitative data
Dataset Size 529.6 MB
4D view
SSBD:OMERO
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# 10569
Dataset Kind Quantitative data
Dataset Size 3.6 GB
4D view
SSBD:OMERO
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# 10570
Dataset Kind Quantitative data
Dataset Size 828.7 MB
4D view
SSBD:OMERO
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# 10571
Dataset Kind Quantitative data
Dataset Size 1.6 GB
4D view
SSBD:OMERO
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# 10572
Dataset Kind Quantitative data
Dataset Size 720.7 MB
4D view
SSBD:OMERO
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# 10573
Dataset Kind Quantitative data
Dataset Size 2.2 GB
4D view
SSBD:OMERO
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# 10574
Dataset Kind Quantitative data
Dataset Size 450.1 MB
4D view
SSBD:OMERO
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# 10575
Dataset Kind Quantitative data
Dataset Size 522.4 MB
4D view
SSBD:OMERO
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# 10576
Dataset Kind Quantitative data
Dataset Size 150.9 MB
4D view
SSBD:OMERO
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# 10577
Dataset Kind Quantitative data
Dataset Size 802.1 MB
4D view
SSBD:OMERO
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# 10578
Dataset Kind Quantitative data
Dataset Size 451.2 MB
4D view
SSBD:OMERO
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# 10579
Dataset Kind Quantitative data
Dataset Size 133.4 MB
4D view
SSBD:OMERO
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# 10580
Dataset Kind Quantitative data
Dataset Size 271.0 MB
4D view
SSBD:OMERO
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# 10581
Dataset Kind Quantitative data
Dataset Size 30.6 MB
4D view
SSBD:OMERO
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# 10582
Dataset Kind Quantitative data
Dataset Size 28.4 MB
4D view
SSBD:OMERO
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# 10583
Dataset Kind Quantitative data
Dataset Size 26.3 MB
4D view
SSBD:OMERO
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# 10584
Dataset Kind Quantitative data
Dataset Size 27.0 MB
4D view
SSBD:OMERO
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# 10585
Dataset Kind Quantitative data
Dataset Size 26.7 MB
4D view
SSBD:OMERO
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# 10586
Dataset Kind Quantitative data
Dataset Size 23.5 MB
4D view
SSBD:OMERO
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# 10587
Dataset Kind Quantitative data
Dataset Size 31.2 MB
4D view
SSBD:OMERO
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# 10588
Dataset Kind Quantitative data
Dataset Size 41.1 MB
4D view
SSBD:OMERO
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# 10589
Dataset Kind Quantitative data
Dataset Size 36.5 MB
4D view
SSBD:OMERO
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# 10590
Dataset Kind Quantitative data
Dataset Size 23.0 MB
4D view
SSBD:OMERO
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# 10591
Dataset Kind Quantitative data
Dataset Size 28.6 MB
4D view
SSBD:OMERO
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# 10592
Dataset Kind Quantitative data
Dataset Size 32.8 MB
4D view
SSBD:OMERO
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# 10593
Dataset Kind Quantitative data
Dataset Size 27.8 MB
4D view
SSBD:OMERO
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# 10594
Dataset Kind Quantitative data
Dataset Size 18.7 MB
4D view
SSBD:OMERO
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# 10595
Dataset Kind Quantitative data
Dataset Size 31.1 MB
4D view
SSBD:OMERO
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# 10596
Dataset Kind Quantitative data
Dataset Size 29.6 MB
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SSBD:OMERO
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# 10597
Dataset Kind Quantitative data
Dataset Size 33.5 MB
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SSBD:OMERO
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# 10598
Dataset Kind Quantitative data
Dataset Size 28.0 MB
4D view
SSBD:OMERO
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# 10599
Dataset Kind Quantitative data
Dataset Size 28.8 MB
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SSBD:OMERO
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# 10600
Dataset Kind Quantitative data
Dataset Size 26.1 MB
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SSBD:OMERO
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# 10601
Dataset Kind Quantitative data
Dataset Size 31.3 MB
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# 10602
Dataset Kind Quantitative data
Dataset Size 33.6 MB
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# 10603
Dataset Kind Quantitative data
Dataset Size 30.2 MB
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SSBD:OMERO
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# 10604
Dataset Kind Quantitative data
Dataset Size 26.8 MB
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# 10605
Dataset Kind Quantitative data
Dataset Size 26.8 MB
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# 10606
Dataset Kind Quantitative data
Dataset Size 34.5 MB
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# 10607
Dataset Kind Quantitative data
Dataset Size 33.1 MB
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# 10608
Dataset Kind Quantitative data
Dataset Size 33.4 MB
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# 10609
Dataset Kind Quantitative data
Dataset Size 42.1 MB
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# 10610
Dataset Kind Quantitative data
Dataset Size 22.0 MB
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# 10611
Dataset Kind Quantitative data
Dataset Size 31.5 MB
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SSBD:OMERO
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# 10612
Dataset Kind Quantitative data
Dataset Size 33.6 MB
4D view
SSBD:OMERO
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# 10613
Dataset Kind Quantitative data
Dataset Size 35.8 MB
4D view
SSBD:OMERO
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# 10614
Dataset Kind Quantitative data
Dataset Size 39.2 MB
4D view
SSBD:OMERO
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# 10615
Dataset Kind Quantitative data
Dataset Size 27.0 MB
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SSBD:OMERO
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# 10616
Dataset Kind Quantitative data
Dataset Size 30.1 MB
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SSBD:OMERO
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# 10617
Dataset Kind Quantitative data
Dataset Size 25.7 MB
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SSBD:OMERO
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# 10618
Dataset Kind Quantitative data
Dataset Size 29.4 MB
4D view
SSBD:OMERO
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# 10619
Dataset Kind Quantitative data
Dataset Size 23.8 MB
4D view
SSBD:OMERO
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# 10620
Dataset Kind Quantitative data
Dataset Size 27.8 MB
4D view
SSBD:OMERO
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# 10621
Dataset Kind Quantitative data
Dataset Size 32.9 MB
4D view
SSBD:OMERO
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# 10622
Dataset Kind Quantitative data
Dataset Size 36.8 MB
4D view
SSBD:OMERO
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# 10623
Dataset Kind Quantitative data
Dataset Size 26.7 MB
4D view
SSBD:OMERO
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# 10624
Dataset Kind Quantitative data
Dataset Size 27.8 MB
4D view
SSBD:OMERO
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# 10625
Dataset Kind Quantitative data
Dataset Size 35.7 MB
4D view
SSBD:OMERO
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# 10626
Dataset Kind Quantitative data
Dataset Size 32.0 MB
4D view
SSBD:OMERO
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# 10627
Dataset Kind Quantitative data
Dataset Size 32.2 MB
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SSBD:OMERO
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# 10628
Dataset Kind Quantitative data
Dataset Size 31.1 MB
4D view
SSBD:OMERO
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# 10629
Dataset Kind Quantitative data
Dataset Size 28.6 MB
4D view
SSBD:OMERO
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# 10630
Dataset Kind Quantitative data
Dataset Size 30.0 MB
4D view
SSBD:OMERO
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# 10631
Dataset Kind Quantitative data
Dataset Size 36.7 MB
4D view
SSBD:OMERO
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# 10632
Dataset Kind Quantitative data
Dataset Size 27.7 MB
4D view
SSBD:OMERO
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# 10633
Dataset Kind Quantitative data
Dataset Size 29.5 MB
4D view
SSBD:OMERO
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# 10634
Dataset Kind Quantitative data
Dataset Size 29.3 MB
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SSBD:OMERO
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# 10635
Dataset Kind Quantitative data
Dataset Size 33.6 MB
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SSBD:OMERO
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# 10636
Dataset Kind Quantitative data
Dataset Size 24.0 MB
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SSBD:OMERO
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# 10637
Dataset Kind Quantitative data
Dataset Size 32.3 MB
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SSBD:OMERO
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# 10638
Dataset Kind Quantitative data
Dataset Size 29.9 MB
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SSBD:OMERO
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# 10639
Dataset Kind Quantitative data
Dataset Size 38.3 MB
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# 10640
Dataset Kind Quantitative data
Dataset Size 35.5 MB
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SSBD:OMERO
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# 10641
Dataset Kind Quantitative data
Dataset Size 33.4 MB
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# 10642
Dataset Kind Quantitative data
Dataset Size 38.5 MB
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# 10643
Dataset Kind Quantitative data
Dataset Size 26.6 MB
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# 10644
Dataset Kind Quantitative data
Dataset Size 29.9 MB
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# 10645
Dataset Kind Quantitative data
Dataset Size 31.5 MB
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# 10646
Dataset Kind Quantitative data
Dataset Size 24.5 MB
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# 10647
Dataset Kind Quantitative data
Dataset Size 23.7 MB
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# 10648
Dataset Kind Quantitative data
Dataset Size 427.8 MB
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# 10649
Dataset Kind Quantitative data
Dataset Size 38.5 MB
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# 10650
Dataset Kind Quantitative data
Dataset Size 38.7 MB
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# 10651
Dataset Kind Quantitative data
Dataset Size 23.8 MB
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# 10652
Dataset Kind Quantitative data
Dataset Size 37.2 MB
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# 10653
Dataset Kind Quantitative data
Dataset Size 28.5 MB
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# 10654
Dataset Kind Quantitative data
Dataset Size 31.4 MB
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# 10655
Dataset Kind Quantitative data
Dataset Size 40.1 MB
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# 10656
Dataset Kind Quantitative data
Dataset Size 32.7 MB
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# 10657
Dataset Kind Quantitative data
Dataset Size 36.6 MB
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# 10658
Dataset Kind Quantitative data
Dataset Size 34.3 MB
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# 10659
Dataset Kind Quantitative data
Dataset Size 30.3 MB
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# 10660
Dataset Kind Quantitative data
Dataset Size 30.2 MB
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# 10661
Dataset Kind Quantitative data
Dataset Size 33.4 MB
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SSBD:OMERO
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# 10662
Dataset Kind Quantitative data
Dataset Size 35.2 MB
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SSBD:OMERO
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# 10663
Dataset Kind Quantitative data
Dataset Size 23.5 MB
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SSBD:OMERO
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# 10664
Dataset Kind Quantitative data
Dataset Size 21.8 MB
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SSBD:OMERO
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