Resources

As of Oct. 3, 2016 there are 458 BDML-files.

OrganismTypeBasedonPaperNumber of BDML-filesNumber of images in SSBDReleased dateUpdate date
M. musculusNucleusMeasurementBashar et al. 201212,800 (.tif)2014/10/03-
M. musculusGene expressionMeasurementMasumoto et al. 2010 8 (OmicsBDML)02014/10/03-
M. musculusGene expressionMeasurementHarima et al. 2013 2146 (.tif)2016/01/18-
M. musculusCell/MoleculeMeasurementOchiai et al. 2015061 (.tif)2016/10/03-
M. musculus (iPS)Cell/ParticleMeasurementTanaka & Fujita 2015 214,573 (.tif)2016/10/03-
D. rerioNucleusMeasurementKeller et al. 2008702013/10/032014/06/18
D. melanogasterNucleusMeasurementKeller et al. 2010202013/10/032014/06/18
C. elegansNucleusMeasurementBao et al. 2006202013/10/032014/06/18
C. elegansNucleusMeasurementKyoda et al. 20131862,221,560 (IPLab format; .ipm)2013/09/022014/06/18
C. elegansNucleusMeasurementToyoshima et al. 20161413,954 (.tif)2016/05/202016/10/03
C. elegansCellMeasurementTakayama et al. 201611977,306 (.tif)2016/10/03-
C. elegansNucleusSimulationKimura & Onami 200510002013/10/032014/06/18
C. elegansBehaviorMeasurementCronin et al. 20051102014/10/03-
D. discoideumMoleculeMeasurementKomatsuzaki et al. 201511,800 (.avi)2015/10/03-
D. discoideum, Cultured cell (rat; PC-12), NAMoleculeMeasurement/SimulationWatabe et al. 2015 441 (.tif)2016/01/182016/10/03
E. coliMoleculeSimulationArjunan & Tomita 2010 102013/09/022014/06/18
Cultured cell (rat; NRK-52E)Cell/MoleculeMeasurementAoki et al. 201308562016/10/03-
Cultured cell (human; HT-1080)CellMeasurementKunida et al. 201202112016/10/03-
NAParticleMeasurementTanaka 201402002016/10/03-

Related papers of resources

  • Ii S, Sugiyama K, Takagi S, Matsumoto Y (2012)
    A computational blood flow analysis in a capillary vessel including multiple red blood cells and platelets. J. Biomech. Sci. Eng., 7(1), 72-83 [J-STAGE].
  • Matsumoto Y, Ii S, Shiozaki S, Sugiyama K, Takagi S (2014)
    Toward the multi-scale simulation for a human body using the next-generation supercompute. Procedia IUTAM, 10, 193-200 [ScienceDirect].
  • Bashar MK, Komatsu K, Fujimori T, Kobayashi TJ (2012)
    Automatic extraction of nuclei centroids of mouse embryonic cells from fluorescence microscopy images. PLoS One, 7(5), e35550 [PubMed].
  • Masumoto KH, Ukai-Tadenuma M, Kasukawa T, Nagano M, Uno KD, Tsujino K, Horikawa K, Shigeyoshi Y, Ueda HR (2010)
    Acute induction of Eya3 by late-night light stimulation triggers TSH╬▓ expression in photoperiodis. Curr. Biol., 20(24), 2199-2206 [PubMed].
  • Harima Y, Takashima Y, Ueda Y, Ohtsuka T, Kageyama R (2013)
    Accelerating the tempo of the segmentation clock by reducing the number of introns in the Hes7 gene. Cell Rep., 3(1), 1-7 [PubMed].
  • Ochiai H, Sugawara T, Yamamoto T (2015)
    Simultaneous live imaging of the transcription and nuclear position of specific genes. Nucleic Acids Res., 43(19), e127 [PubMed].
  • Tanaka Y, Fujita H (2015)
    Fluid driving system for a micropump by differentiating iPS cells into cardiomyocytes on a tent-like structure. Sens. Actuators B Chem., 210(1), 267-272 [ScienceDirect].
  • Keller PJ, Schmidt AD, Wittbrodt J, Stelzer EHK (2008)
    Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy. Science, 322(5904), 1065-1069 [PubMed].
  • Keller PJ, Schmidt AD, Santella A, Khairy K, Bao Z, Wittbrodt J, Stelzer EHK (2010)
    Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy. Nat. Methods, 7(8), 637-642 [PubMed].
  • Bao Z, Murray JI, Boyle T, Ooi SL, Sandel MJ, Waterston RH (2006)
    Automated cell lineage tracing in Caenorhabditis elegans. Proc. Natl. Acad. Sci. U.S.A., 103(8), 2707-2712 [PubMed].
  • Kyoda K, Adachi E, Masuda E, Nagai Y, Suzuki Y, Oguro T, Urai M, Arai R, Furukawa M, Shimada K, Kuramochi J, Nagai E, Onami S (2013)
    WDDD: Worm Developmental Dynamics Database. Nucleic Acids Res., 41, D732-D737 [PubMed].
  • Toyoshima Y, Tokunaga T, Hirose O, Kanamori M, Teramoto T, Jang MS, Kuge S, Ishihara T, Yoshida R, Iino Y (2016)
    Accurate automatic detection of densely distributed cell nuclei in 3D space. PLoS Comput. Biol., 12(6), e1004970 [PubMed].
  • Takayama J, Onami S. (2016)
    The sperm TRP-3 channel mediates the onset of a Ca(2+) wave in the fertilized C. elegans oocyte. Cell Rep., 15(3), 625-637. [PubMed].
  • Kimura A, Onami S (2005)
    Computer simulations and image processing reveal length-dependent pulling force as the primary mechanism for C. elegans male pronuclear migration. Dev. Cell, 8(5), 765-775 [PubMed].
  • Cronin CJ, Mendel JE, Mukhtar S, Kim YM, Stirbl RC, Bruck J, Sternberg PW (2005)
    An automated system for measuring parameters of nematode sinusoidal movement. BMC Genet., 6, 5 [PubMed].
  • Komatsuzaki A, Ohyanagi T, Tsukasaki Y, Miyanaga Y, Ueda M, Jin T (2015)
    Compact halo-ligand-conjugated quantum dots for multicolored single-molecule imaging of overcrowding GPCR proteins on cell membranes. Small, 11(12), 1396-1401 [PubMed].
  • Watabe M, Arjunan SN, Fukushima S, Iwamoto K, Kozuka J, Matsuoka S, Shindo Y, Ueda M, Takahashi K (2015)
    A computational framework for bioimaging simulation. PLoS One, 10(7), e0130089 [PubMed].
  • Arjunan SNV, Tomita M (2010)
    A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation. Syst. Synth. Biol., 4(1), 35-53 [PubMed].
  • Aoki K, Kumagai Y, Sakurai A, Komatsu N, Fujita Y, Shionyu C, Matsuda M (2013)
    Stochastic ERK activation induced by noise and cell-to-cell propagation regulates cell density-dependent proliferation. Mol. Cell, 52(4), 529-540 [PubMed].
  • Kunida K, Matsuda M, Aoki K (2012)
    FRET imaging and statistical signal processing reveal positive and negative feedback loops regulating the morphology of randomly migrating HT-1080 cells. J. Cell Sci., 125(10), 2381-2392 [PubMed].
  • Tanaka Y (2014)
    A peristaltic pump integrated on a 100% glass microchip using computer controlled piezoelectric actuators. Micromachines, 5(2), 289-299 [Micromachines].