Method Summary
Paper information

Release 2024-07-01
Title Rac1/Rac3-double knockout cochlear hair cells
Organism mouse cochlea
Size 51.4 MB
Method Summary See details in Nakamura, et. al. (2023) J Mol Med (Berl).
Paper Information Nakamura T et. al. (2023), J Mol Med (Berl)
doi: 10.1007/s00109-023-02317-4 pmid: 37204479

Release 2024-06-10
Title Dataset of actin nanocluster dynamics during Drosophila tracheal tubulogenesis
Organism Drosophila melanogaster
Size 10.1 GB
Method Summary See details in Sekine et al., (2023)
Paper Information Sekine S et. al. (2024), Nat Commun 15(1), 464
doi: 10.1038/s41467-023-44684-z pmid: 38267421

Release 2024-06-08
Title Expression patterns of Osiris family genes in the pupal head of Drosophila
Organism Drosophila melanogaster
Size 3.0 GB
Method Summary See details in "Sun Z, Inagaki S, Miyoshi K, Saito K, Hayashi S. Osiris gene family defines the cuticle nanopatterns of Drosoph…
Paper Information Sun Z et. al. (2024), Genetics
doi: 10.1093/genetics/iyae065 pmid: 38652268

Release 2024-06-04
Title Neuropeptide gene expression atlas in the adult zebrafish brain
Organism Danio rerio
Size 108.5 GB
Method Summary
Paper Information Hiraki-Kajiyama T et. al. (2024), J Comp Neurol 532(6), e25619
doi: 10.1002/cne.25619 pmid: 38831653

Release 2024-05-17
Title SEM imege of cancer cells adhered on the track etched membrane
Organism Homo sapiens
Size 187.7 MB
Method Summary Four cell lines (MCF10A, MCF7, MDA-MB-231, and PC-3 cells) were adhered on the track-etched membrane (Merck, VCTP04700) precoat…
Paper Information Shiomi A et. al. (2024), Nat Commun 15(1), 3812
doi: 10.1038/s41467-024-48088-5 pmid: 38760380

Release 2024-04-08
Title Dataset for "Live-cell fluorescence imaging and optogenetic control of PKA kinase activity in fission yeast Schizosaccharomyces pombe."
Organism Schizosaccharomyces pombe
Size 84.4 GB
Method Summary See details in Sakai et al., bioRxiv, 2024
Paper Information Sakai K et. al. (2024), Yeast
doi: 10.1002/yea.3937 pmid: 38583078

Release 2024-01-15
Title Dataset for "Live-cell imaging provides direct evidence for a threshold in CDK activity at the G2/M transition."
Organism Schizosaccharomyces pombe
Size 76.2 GB
Method Summary See details in Sugiyama et. al., bioRxiv. 2023
Paper Information Hironori Sugiyama et. al. (2023/01/01), 2023.03.26.534249
doi: 10.1101/2023.03.26.534249 Sugiyama H et. al. (2024), Dev Cell
doi: 10.1016/j.devcel.2023.12.014 pmid: 38228139

Release 2023-08-15
Title x-y coordinates of Caenorhabditis elegans centroids stimulated with electric shock
Organism Caenorhabditis elegans
Size 38.7 MB
Method Summary
Paper Information Tee LF et. al. (2023), Genetics
doi: 10.1093/genetics/iyad148 pmid: 37595066

Release 2023-08-07
Title All four knockout of ErbB-family genes delineates their roles in proliferation, survival, and collective cell migration of epithelial cells.
Organism canis familiaris
Size 64.4 GB
Method Summary Most of the time-lapse images were obtained with epifluorescence microscopy. Some of the experiments were done with confocal mi…
Paper Information Matsuda K et. al. (2023), J Cell Sci
doi: 10.1242/jcs.261199 pmid: 37519219

Release 2023-07-20
Title Identifying a lung stem cell subpopulation by combining single-cell morphometrics, organoid culture, and transcriptomics
Organism Mus musculus, Homo sapiens
Size 6.5 GB
Method Summary
Paper Information Fujimura T et. al. (2023), Stem Cells
doi: 10.1093/stmcls/sxad044 pmid: 37468433

Release 2023-06-09
Title Nuclear shape of excitatory neurons in the visual cortex upon visual stimulation of young and aged mice
Organism Mus Musculus
Size 2.5 GB
Method Summary See detail in Frey et al., bioRxiv, 2022
Paper Information Tanita Frey et. al. (2022/01/01), 2022.08.22.504704
doi: 10.1101/2022.08.22.504704

Release 2023-06-07
Title Imaging data in the paper, "Activity-dependent local protection and lateral inhibition mediate synaptic competition in developing mitral cells" (Fujimoto et al., 2023).
Organism Mus musculus
Size 752.0 GB
Method Summary
Paper Information Fujimoto S et. al. (2023), Dev Cell
doi: 10.1016/j.devcel.2023.05.004 pmid: 37290446

Release 2023-04-26
Title Fiber photometry traces of the kisspeptin neurons in the arcuate nucleus of the hypothalamus in young and aging mice
Organism Mus musculus
Size 16.1 GB
Method Summary See detail in Dynamics of Pulsatile Activities of Arcuate Kisspeptin Neurons in Aging Female Mice. Goto T et al. (2022), BioRxiv
Paper Information Teppei Goto et. al. (2023/01/01), 2022.08.08.503241
doi: 10.1101/2022.08.08.503241 Goto T et. al. (2023), Elife 12
doi: 10.7554/eLife.82533 pmid: 37223988

Release 2023-04-13
Title Bright-field images of the liverwort Marchantia polymorpha ssp. ruderalis in gemmalings (dorsal view).
Organism Marchantia polymorpha
Size 32.2 GB
Method Summary
Paper Information

Release 2023-03-09
Title Epidermal growth factor receptor signaling protects epithelia from morphogenetic instability and tissue damage in Drosophila
Organism Drosophila melanogaster
Size 146.3 GB
Method Summary Described in the manuscript.
Paper Information Yoshida, Kentaro and Hayashi, Shigeo (2022/01/01), 2022.08.28.505615
doi: 10.1101/2022.08.28.505615 Yoshida K and Hayashi S (2023), Development 150(5)
doi: 10.1242/dev.201231 pmid: 36897356

Release 2022-12-15
Title Bright-field time-lapse images of live murine immune-related cells
Organism Mus musculus
Size 798.8 MB
Method Summary Iamges were captured using an inverted optical microscope (Eclipse Ti2-E, Nikon) with an 20X objective lens (CFI Plan Apochroma…
Paper Information Jin J et. al. (2023), Proc Natl Acad Sci U S A 120(1), e2210283120
doi: 10.1073/pnas.2210283120 pmid: 36577074

Release 2022-09-29
Title Imaging dataset of migrating MDCK cells and wounded mouse ear skin.
Organism Canis familiaris, Mus musculus
Size 81.9 GB
Method Summary See details in Hino, N., Matsuda, K., Jikko, Y., Maryu, G., Sakai, K., Imamura, R., Tsukiji, S., Aoki, K., Terai, K., Hirashima…
Paper Information Hino N et. al. (2022), Dev Cell 57(19), 2290-2304.e7
doi: 10.1016/j.devcel.2022.09.003 pmid: 36174555

Release 2022-06-30
Title Cell membrane images, restored images, and segmentation results of 52 C. elegans embryos.
Organism Caenorhabditis elegans
Size 236.3 GB
Method Summary Image processing, deep learning
Paper Information Azuma, Yusuke et. al. (2023), Frontiers in Bioinformatics 3
doi: 10.3389/fbinf.2023.1082531

Release 2022-04-21
Title Quantitative live-cell imaging of GPCR downstream signaling dynamics.
Organism Homo sapiens
Size 10.3 GB
Method Summary Tany R, Goto Y, Kondo Y, Aoki K. Quantitative live-cell imaging of GPCR downstream signaling dynamics. Biochem J. 2022 Apr 29;4…
Paper Information Tany R et. al. (2022), Biochem J 479(8), 883-900
doi: 10.1042/BCJ20220021 pmid: 35383830

Release 2022-04-18
Title Raman imaging in HeLa cells treated with D-alkyne-tagged C18FAs
Organism H. sapiens
Size 4.4 MB
Method Summary Egoshi S, Dodo K, Ohgane K, Sodeoka M. Deuteration of terminal alkynes realizes simultaneous live cell Raman imaging of similar…
Paper Information Egoshi S et. al. (2021), Org Biomol Chem 19(38), 8232-8236
doi: 10.1039/d1ob01479j pmid: 34528645

Release 2022-03-23
Title Adult zebrafish's telencephalic neural activity and behavior data during the GO/NOGO tasks in the virtual reality environment.
Organism Danio rerio
Size 581.7 GB
Method Summary Torigoe M, Islam T, Kakinuma H, Fung CCA, Isomura T, Shimazaki H, Aoki T, Fukai T, Okamoto H. Zebrafish capable of generating f…
Paper Information Torigoe M et. al. (2021), Nat Commun 12(1), 5712
doi: 10.1038/s41467-021-26010-7 pmid: 34588436

Release 2022-03-09
Title Raman imaging in WI-38/VA-13 cells treated with 100 µM all-D-GLA
Organism H. sapiens
Size 4.7 MB
Method Summary Dodo K, Sato A, Tamura Y, Egoshi S, Fujiwara K, Oonuma K, Nakao S, Terayama N, Sodeoka M. Synthesis of deuterated γ-linolenic a…
Paper Information Dodo K et. al. (2021), Chem Commun (Camb) 57(17), 2180-2183
doi: 10.1039/d0cc07824g pmid: 33527102

Release 2022-01-31
Title Imaging data sets of ATDC5 cells and fetal growth plates
Organism Mus musculus
Size 28.8 GB
Method Summary See details in Hirota K, Hirashima T, Horikawa K, Yasoda A, Matsuda M. C-type natriuretic peptide-induced PKA activation promot…
Paper Information Hirota K et. al. (2022), Endocrinology 163(3)
doi: 10.1210/endocr/bqac005 pmid: 35041746

Release 2021-11-29
Title Imaging dataset for "Near-infrared imaging in fission yeast by genetically encoded biosynthesis of phycocyanobilin"
Organism Schizosaccharomyces pombe, Saccharomyces cerevisiae, Homo Sapiens
Size 75.6 GB
Method Summary See details in Sakai, et al. (2021), Journal of Cell Science
Paper Information Sakai K et. al. (2021), J Cell Sci 134(24)
doi: 10.1242/jcs.259315 pmid: 34806750

Release 2021-11-25
Title Swimming behaviors of C. elegans in various genetic background cultured in different food conditions; cultured with OP50, 1g/L glucose, or no nutrients (M9 buffer)
Organism Caenorhabditis elegans
Size 48.6 GB
Method Summary Arata Y, Shiga I, Ikeda Y, Jurica P, Kimura H, Kiyono K, Sako Y. Insulin signaling shapes fractal scaling of C. elegans behavio…
Paper Information Arata Y et. al. (2022), Sci Rep 12(1), 10481
doi: 10.1038/s41598-022-13022-6 pmid: 35729173

Release 2021-11-09
Title Imaging dataset for "Optogenetic relaxation of actomyosin contractility uncovers mechanistic roles of cortical tension during cytokinesis."
Organism xenopus laevis, canis familiaris, mus musculus
Size 17.8 GB
Method Summary See details in Yamamoto K, Miura H, Ishida M, Mii Y, Kinoshita N, Takada S, Ueno N, Sawai S, Kondo Y, Aoki K. Optogenetic relax…
Paper Information Yamamoto K et. al. (2021), Nat Commun 12(1), 7145
doi: 10.1038/s41467-021-27458-3 pmid: 34880255

Release 2021-10-20
Title Post-hoc Correction of Chromatic Aberrations in Large-scale Volumetric Images in Confocal Microscopy
Organism Mus musculus
Size 236.2 GB
Method Summary See also Leiwe MN, Fujimoto S and Imai T (2021) Post hoc Correction of Chromatic Aberrations in Large-Scale Volumetric Images i…
Paper Information Leiwe MN et. al. (2021), Front Neuroanat 15, 760063
doi: 10.3389/fnana.2021.760063 pmid: 34955764

Release 2021-10-18
Title Redundant and specific roles of EGFR ligands in the ERK activation waves during collective cell migration of MDCK cells
Organism canis familiaris
Size 90.3 GB
Method Summary See details in Lin S, Hirayama D, Maryu G, Matsuda K, Hino N, Deguchi E, Aoki K, Iwamoto R, Terai K, Matsuda M. Redundant roles…
Paper Information Lin S et. al. (2022), Life Sci Alliance 5(1)
doi: 10.26508/lsa.202101206 pmid: 34667080

Release 2021-10-01
Title Micro-topographical guidance of macropinocytic signaling patches
Organism Dictyostelium discoideum
Size 6.4 GB
Method Summary See details in Honda et. al. (2021) PNAS
Paper Information Honda G et. al. (2021), Proc Natl Acad Sci U S A 118(50)
doi: 10.1073/pnas.2110281118 pmid: 34876521

Release 2021-09-30
Title A set of imaging data related to the development of trans-scale scope and its application to biological study
Organism Mouse, Canis Lupus Familiaris, Homo sapiens, Dictyostelium discoideum
Size 602.5 GB
Method Summary Ichimura, T., Kakizuka, T., Horikawa, K. et al. Exploring rare cellular activity in more than one million cells by a transscale…
Paper Information Ichimura T et. al. (2021), Sci Rep 11(1), 16539
doi: 10.1038/s41598-021-95930-7 pmid: 34400683 Ichimura, T. et. al. (2021/01/01), 2020.06.29.179044
doi: 10.1101/2020.06.29.179044

Release 2021-09-11
Title See the paper titled “Metastatic tumor cells evade pulmonary NK cell-mediated killing by thrombin-mediated loss of CD155/PVR/Necl-5. ”
Organism Mus musculus
Size 244.1 GB
Method Summary Two photon microscopy, Lung intravital imaging, Bioluminescence imaging
Paper Information Ichise H et. al. (2022), Elife 11
doi: 10.7554/eLife.76269 pmid: 35113018

Release 2021-07-01
Title Two photon fluorescent images from hyBRET-AMPK and GO-ATeam2 retinal explants.
Organism Mus musculus
Size 11.9 GB
Method Summary Two photon microscopy, live ex vivo culture
Paper Information He J et. al. (2021), FASEB J 35(9), e21880
doi: 10.1096/fj.202101121R pmid: 34449091

Release 2021-06-09
Title Live imaging data of developing hair follicles in an article “Tracing the origin of hair follicle stem cells” (Morita et al., 2021).
Organism Mus musculus
Size 708.1 GB
Method Summary See details in Morita, R., Sanzen, N., Sasaki, H. et al. Tracing the origin of hair follicle stem cells. Nature (2021).
Paper Information Morita R et. al. (2021), Nature 594(7864), 547-552
doi: 10.1038/s41586-021-03638-5 pmid: 34108685

Release 2021-05-12
Title Comparative mapping of crawling-cell morphodynamics in deep learning-based feature space
Organism Homo sapiens, Unknown (fish keratocyte), Dictyostelium discoideum
Size 4.9 GB
Method Summary Deep Learning based morphology analysis and phase-field morpho-dynamics simulation for a fast migrating cell
Paper Information Imoto D et. al. (2021), PLoS Comput Biol 17(8), e1009237
doi: 10.1371/journal.pcbi.1009237 pmid: 34383753

Project ssbd-repos-000170 SSBD:database
Release 2021-05-11
Title Mapping the molecular and structural specialization of the skin basement membrane for inter-tissue interactions
Organism Mus musculus
Size 2.9 GB
Method Summary See details in Tsutsui, K., Machida, H., Nakagawa, A. et al. Mapping the molecular and structural specialization of the skin ba…
Paper Information Tsutsui K et. al. (2021), Nat Commun 12(1), 2577
doi: 10.1038/s41467-021-22881-y pmid: 33972551

Release 2021-04-12
Title Time-lapse images of ERK activity in embryonic murine trachea published in (2020, Yoshida et al., Front Cell Dev Biol)
Organism Mus musculus
Size 62.2 GB
Method Summary See details in 2020, Yoshida et al., Frontiers in Cell and Developmental Biology
Paper Information Yoshida T et. al. (2020), Front Cell Dev Biol 8, 585640
doi: 10.3389/fcell.2020.585640 pmid: 33195234

Release 2021-03-29
Title Imaging and other-related data of neurogenic tagging mouse lines.
Organism Mus musculus (NCBI:txid10090)
Size 1.6 TB
Method Summary See details in Hirata et al., NeuroGT: A brain atlas of neurogenic tagging CreER drivers for birthdate-based classification and…
Paper Information Hirata T et. al. (2021), Cell Rep Methods 1(3), 100012
doi: 10.1016/j.crmeth.2021.100012 pmid: 35474959

Release 2021-02-17
Title Imaging data of the oocytes in C. elegans adults
Organism C. elegans
Size 43.0 MB
Method Summary See details in Imakubo et al. (2021) BMC Bioinformatics 22(1):73.
Paper Information Imakubo M et. al. (2021), BMC Bioinformatics 22(1), 73
doi: 10.1186/s12859-021-03990-3 pmid: 33596821

Release 2020-10-30
Title Sets of image data of mouse mitral cells genetically labeled with utero electroporation.
Organism Mus musculus
Size 162.2 GB
Method Summary See detail in Aihara S, Fujimoto S, Sakaguchi R, Imai T. BMPR-2 gates activity-dependent stabilization of primary dendrites dur…
Paper Information Aihara S et. al. (2021), Cell Rep 35(12), 109276
doi: 10.1016/j.celrep.2021.109276 pmid: 34161760

Release 2020-07-23
Title Bidirectional Wnt signaling between endoderm and mesoderm confers tracheal identity in mouse and human cells
Organism Mus Musculus, Homo sapiens
Size 6.9 GB
Method Summary "Methods Mice All mouse experiments were approved by the Institutional Animal Care and Use Committee of RIKEN Kobe Branch. Mi…
Paper Information Kishimoto K et. al. (2020), Nat Commun 11(1), 4159
doi: 10.1038/s41467-020-17969-w pmid: 32855415

Release 2020-07-22
Title Time-lapse images of ERK activity in MDCK cells published in (2020, Boocock et al., Nat Phys)
Organism Canis lupus familiaris
Size 48.8 GB
Method Summary See detail in Boocock et al. (2021) Nature Physics 17, 267-274
Paper Information Boocock, Daniel et. al. (2021), Nature Physics 17(2), 267-274
doi: 10.1038/s41567-020-01037-7

Release 2020-07-09
Title A set of calcium imaging data in the olfactory system of M. musculus adult
Organism Mus musculus
Size 33.0 GB
Method Summary See details in Inagaki et al. (2020) Cell Rep., 31(13): 107814.
Paper Information Inagaki S et. al. (2020), Cell Rep 31(13), 107814
doi: 10.1016/j.celrep.2020.107814 pmid: 32610120

Release 2020-06-23
Title Raw data of an article “Multiple types of navigational information are diffusely and independently encoded in the population activities of the dentate gyrus neurons” (Murano et al., 2020)
Organism Mus musculus
Size 4.9 TB
Method Summary See details in Murano T, Nakajima R, Nakao A, Hirata N, Amemori S, Murakami A, Kamitani Y, Yamamoto J, Miyakawa T. Multiple typ…
Paper Information Murano T et. al. (2022), Proc Natl Acad Sci U S A 119(32), e2106830119
doi: 10.1073/pnas.2106830119 pmid: 35930667 Murano, Tomoyuki et. al. (2020/01/01), 2020.06.09.141572
doi: 10.1101/2020.06.09.141572

Release 2019-06-17
Title A set of RNA-FISH and immunofluorescence images of Xist/Tsix expression during peri-implantation embryoic development using whole-mount 3D RNA-FISH
Organism M. musculus
Size 7.0 GB
Method Summary See details in Shiura et al. (2019) Scientific Reports, 9(1): 3637.
Paper Information Shiura H and Abe K (2019), Sci Rep 9(1), 3637
doi: 10.1038/s41598-019-38807-0 pmid: 30842444

Release 2019-06-13
Title Time-lapse 3D imaging data of cell nuclei
Organism Caenorhabditis elegans, Homo sapiens
Size 3.1 GB
Method Summary See details in Wen et al. (2021) eLife 2021;10:e59187 DOI: 10.7554/eLife.59187
Paper Information Wen C et. al. (2021), Elife 10
doi: 10.7554/eLife.59187 pmid: 33781383

Release 2019-04-19
Title A set of time-lapse imaging data of the C. elegans adults during swimming
Organism C. elegans
Size 17.6 GB
Method Summary Long-term video recording, Microfluidic device
Paper Information Ikeda Y et. al. (2020), Sci Rep 10(1), 14775
doi: 10.1038/s41598-020-70319-0 pmid: 32901071

Release 2019-03-26
Title A set of transverse sections of teleost fish vertebral bodies
Organism M. cinereus, S. melanostictus, K. punctatus, P. altivelis altivelis, L. setigerus, L. litulon, C. abei, Z. nebulosa, Z. faber, M. sagifue, C. saira, H. hilgendorfii, S. oblongus, S. zonatus, C. spinosus, A. hanedai, T. japonicus, P. major, S. japonica, H. typus, S. forsteni, S. pinguis, R. prometheoides, S. japonicus, T. orientalis, T. tonggol, P. olivaceus, H. dubius, M. uradoi, T. pardalis, T snyderi, T. stictonotus
Size 29.9 GB
Method Summary See details in Sakashita et al. (2019) doi: 10.1002/jmor.20983
Paper Information Sakashita M et. al. (2019), J Morphol 280(6), 778-795
doi: 10.1002/jmor.20983 pmid: 30945336

Release 2018-11-07
Title A set of imaging data of neuronal circuits labeling with fluorescent proteins in M. musculus
Organism M. musculus
Size 21.7 GB
Method Summary See details in Sakaguchi et al., eLife
Paper Information Sakaguchi R et. al. (2018), Elife 7
doi: 10.7554/eLife.40350 pmid: 30454553

Release 2017-11-14
Title A set of calcium imaging data in the olfactory system of M. musculus adult
Organism M. musculus
Size 30.9 GB
Method Summary See details in Ryo Iwata, Hiroshi Kiyonari, Takeshi Imai (2017) Neuron, 96(5): 1139-1152.
Paper Information Iwata R et. al. (2017), Neuron 96(5), 1139-1152.e7
doi: 10.1016/j.neuron.2017.11.008 pmid: 29216451

Release 2017-03-17
Title A set of BDML file for digitized cellular dynamics of a C. elegans embryo
Organism C. elegans
Size 76.1 MB
Method Summary See details in Azuma and Onami (2017) BMC Bioinformatics 18, 307.
Paper Information Azuma Y and Onami S (2017), BMC Bioinformatics 18(1), 307
doi: 10.1186/s12859-017-1717-6 pmid: 28629355

Project Ce_NEU_TY SSBD:database
Release 2016-05-22
Title A set of BDML files for quantitative information about neuronal nuclei in C. elegans adult
Organism C. elegans
Size 67.8 MB
Method Summary See details in Toyoshima et al. (2016) PLoS Computational Biology, 12(6): e1004970
Paper Information Toyoshima Y et. al. (2016), PLoS Comput Biol 12(6), e1004970
doi: 10.1371/journal.pcbi.1004970 pmid: 27271939