Communal Microscope Facilities

ESB has a transmission electron microscope, scanning electron microscope, two confocal laser-scanning microscopes, and a high-speed camera. The facility is available for use by all qualified faculty, students, and researchers at SOKENDAI, as well as collaborators from other institutes.

terms & conditions pdf(xxkb)
application form word(xxKB), pdf(xxKB)
For detailed information, please contact:
Atsuko Matsushita []

1Transmission Electron Microscope

We support conventional EM and immunocytochemistry from tissue preparation to image acquisition and analysis.
Specimen examples: insect compound eyes, CNS of mammals and fish, and reproductive organ of mice
Location: Sendo-ken bldg. Room 120

  • Transmission electron microscope(Hitachi H-7650)
  • Two Digital CCD cameras (Seika Digital Image Corp.)
    • Morada: 11MegaPixel Side-mounted CCD camera (Max. 2672 x 4008 pixel)
    • Quemesa: 11MegaPixel Bottom-mounted CCD camera (Max. 4008 x 2664 pixel)
    • imaging software: iTEM (image acquisition, processing, morphometry, etc.)
    • Common file formats for exporting image data
  • Ultramicrotome (Leica UCT)
  • The facility is also equipped with a light microscope (Olympus BX51 (Brightfield/ fluorescence/ Nomarski DIC) with a digital camera (Olympus DP71, software cellSens), and a PC for iTEM analysis.

Transmission Electron Microscope equipped with a CCD camera (Hitachi H-7650 and Morada)

Installed in 2006


Ultramicrotome (Leica UCT)


2Scanning Electron Microscope

We support whole general protocol from specimen preparation to image scanning.
Specimen examples: insects, archaeological animal/plant remains and their replicas, tips of glass electrodes
Location: Sendo-ken bldg. Room 118

  • Scanning Electron Microscope (JEOL JSM-6490LV)
    • Secondary-electron and backscatter-electron images at High-Vacuum mode
    • Backscatter-electron images at Low-Vacuum mode
    • Analyses with topography image and composition images at backscatter-electron detection mode
    • Large specimen (< 85 mm) available
    • Common file formats for saving/exporting files
  • Ion Sputter Coater(Hitachi E-1045)
    • Coats those non-conductive specimens with platinum sputtering or carbon evaporation to prevent charge-up under SEM
  • Freeze Dryer(Hitachi ES-2030)
    • Removes water from wet specimen by sublimation under frozen-vacuumed condition, preventing specimen distortion under SEM

Scanning Electron Microscope (JEOL JSM-6490LV)

Installed in 2008


Ion Sputter Coater(Hitachi E-1045)


Freeze Dryer(Hitachi ES-2030)


3Confocal Laser Scanning Microscope (Zeiss)

We support the use of this confocal laser-scanning microscope, especially for 3D-image acquisitions of nuclear architecture, chromosome territories, genes, and other molecules within cell nuclei by multi-color visualization techniques.

Specimen examples: Chromosomes from mouse tissue, HeLa cells, and human lymphocyte cell lines
Location: Sendo-ken bldg. Room 211

  • Confocal laser scanning microscope(Carl Zeiss LSM510META)
    • Laser sources (fine-tuned by AOTF)
      1. Ar458/477/488/514nm
      2. HeNe543nm
      3. HeNe633nm
    • META multi (32) channel detector & high-sensitive PMT detector
    • High-speed acquisition of Lambda Stack function, Metatracking scanning mode, and Emission Fingerprinting function.
    • ROI (region of interest) scanning for specimen protection
    • Photo-bleaching analyses such as FRAP and FLIP are available.
    • Stack Images are saved in Carl Zeiss LSM browser (LSM5) format; Common file formats for exporting files
    • ReUse function: 1-click to replicate parameters for image acquisition

Confocal Laser Scanning Microscope(Carl Zeiss LSM510META)

Installed in 2004


4Confocal laser scanning microscope system (Nikon)

We provide technical supports for various imaging such as multicolor/DIC imaging of either 2D or 3D, simultaneous acquisition of 32-ch spectral images, time-lapse imaging, and photoactivation imaging, by using Nikon A1Rsi configured with Ti-E.
Specimen examples: Neurons of various species, such as insects, echinoderms, and fish; developing echinoderm embryos and fish embryos; photoactivation imaging of algae
Location: Sendo-ken bldg. Room 218

  • Confocal laser scanning microscope (Nikon Ti-E & A1Rsi)
    • Laser sources (fine-tuned by AOTF):
      1. LD 405 nm
      2. multi-Ar 457/477/488/514 nm
      3. DPSS 561 nm
      4. LD 638 nm
    • Inverted light microscope (ECLIPSE Ti-E); motorized stage and fluorescence filters, "Perfect focus system" for automatically correcting focus drift
    • High-resolution with a galvano scanner (Max. 4096 x 4096 pixels),
    • High-speed with a resonant scanner (512 x 512 pixels, 24 frame/sec),
    • Hybrid scanner for ultrafast photoactivation imaging
    • Automatic Enhanced Resolution imaging (NIS-Elements C-ER): Higher resolution images by just 1-click operation (Upgraded in March 2016)
    • Common file formats (avi, tiff, jpg) are available as well as nd2.
  • The facility is also equipped with a stereoscope for sample preparation, incubator (with light/temperature controller) for temporal incubation, and PC for image analysis.
  • Light microscope (Olympus BX51, fluorescence/Nomarski DIC/phase contrast) with a digital camera (Olympus DP72)
    - Available for preliminary check of the sample. (in the first room of Room 218)

Confocal laser scanning microscope (Nikon Ti-E & A1Rsi)

Installed in 2010


Light microscope (Olympus BX51, with DP72)


5High-speed camera (Photoron FASTCAM-Max II)

Recorded example: a flying butterfly
Location: Sendo-ken bldg. Room 118. All devices are housed in one cart, it is available everywhere to go within the campus.

High-speed camera (Photoron FASTCAM-MAX, FASTCAM-MAX II)

Installed in 2010

  1. Two camera heads:
  2. Tripod
  3. Memory: Standard 2.6GB (1sec, at full size & 2000fps), Max 8GB (3.1sec), connectable to PC and a monitor
  4. PC for camera controller, data storing: Windows XP, data transfer by optical cable transmission system
  5. monitor, keyboard, and mouse
Color imaging
High-sensitive sensor, for low light condition
Sensor C-MOS image sensors
Max resolution 1024 x 1024 pixel, color 1024 x 1024 pixel, monochrome
Frame rate 2000 frame/sec (fullframe)
Camera mount C-mount and Nikon F-mount, available for lens and microscopes