PCIC

Plant Cell Imaging Center

Bringing modern imaging technologies to plant biologists at all levels of expertise.

Driving Breakthrough Science

We provide researchers with access to high-resolution fluorescence microscopes, including a confocal microscope with spectral and quantitative imaging capabilities.

Image link

The facility’s instrumentation is optimized for analyzing plant cellular processes, and the center is dedicated to bringing modern imaging technologies to plant biologists at all levels of expertise.

Training and assistance with the use of the microscopes, software, and data analysis are provided. For more information, contact PCIC.

To schedule an appointment for training with microscope use, or for questions, please contact email, call (607) 254-4436, or come to the center between the hours of 9 am and 1 pm. The facility is located on the first floor of BTI (room 104B).

Funding for the purchase of the microscopes was provided by the National Science Foundation Major Research Instrumentation Program (NSF DBI-0618969).

Available Microscopes

The Leica SP5 confocal system has eight visible laser lines provided by a multiline argon laser, a Diode-pumped solid state laser, and orange and red helium neon lasers. In addition, a UV diode laser provides excitation at 405 nm thus enabling the imaging of dyes such as DAPI and the blue fluorescent proteins

Laser Wavelength
  • Near UV Diode: 405 nm
  • Argon: 458 nm, 476 nm, 488 nm, 496 nm, 514 nm
  • DPSS (Diode-Pumped Solid State): 561 nm
  • HeNe Orange (Helium-Neon): 594 nm
  • HeNe red (Helium-Neon): 633 nm

The laser lines are readily controlled by acousto-optical tunable filters (AOTF) and the combination of the acousto-optical beam splitter (AOBS), and the fully tunable spectral detectors provide maximal flexibility for the detection of dyes/fluorescent proteins with closely overlapping emission characteristics.

The three spectral confocal channels and two new HyD (hybrid detector) and a transmitted light channel permit the simultaneous capture of five fluorescent signals plus DIC.

This SP5 system is equipped with a conventional scanner and a high-speed “resonant” scanner capable of scanning up to twenty-five frames/second (512 x 512 format). The confocal system is attached to a Leica DM 6000 fully automated upright microscope with high numerical aperture oil and water immersion objectives and a SuperZ galvonometer-controlled stage.

Objectives
10X Dry
  • Magnification / Aperture: 10X / 0.40
  • Type: HC PL APO CS
20X Water
  • Magnification / Aperture: 20X / 0.70
  • Type: HC PL APO CS
40X Dry
  • Magnification / Aperture: 40X / 0.85
  • Type: HCX PL APO CS
40X Oil
  • Magnification / Aperture: 40X / 1.25-0.75
  • Type: HCX PL APO CS
63X Oil
  • Magnification / Aperture: 63X / 1.40-0.60
  • Type: HCX PL APO CS
63X Water
  • Magnification / Aperture: 63X / 1.20
  • Type: HCX PL APO
100X Oil
  • Magnification / Aperture: 100X / 1.44
  • Type: HCX PL APO

The microscope is equipped with a UV light source (Metal Halogenide) and five filter cubes (UV, green BP, green LP, red LP, and red BP):

Filter Cube A
  • Excitation filter: BP 340-380
  • Emission filter: LP 425
Filter Cube 13
  • Excitation filter: BP 450-490
  • Emission filter: LP 515
Filter Cube GFP
  • Excitation filter: BP 450-490
  • Emission filter: BP 500-550
Filter Cube N2,1
  • Excitation filter: BP 515-560
  • Emission filter: LP 590
Filter Cube N2,1
  • Excitation filter: BP 546/12
  • Emission filter: BP 580-620
 

Training is required, and the training fee is $110 per user. This covers a three-hour training session as well as assistance when using the microscope.

The usage fee is $28.50 per hour.

The Olympus SZX12 is a stereoscope with a long working distance and wide zoom range. It is equipped with DFPLFL 0.5X PF, DFPLAPO 1.2X, and DFPLFL 1.6X PF objectives coupled with 10 X eyepieces (Zoom range to 108X). At present the two parfocal objectives (0.5X and 1.6X) are mounted on a revolving nosepiece that allows easy switching between lenses and easy adjustments of focus. If you need to use 1.2X objective please contact us for the switch.

It is mounted on a transmitted light base and has dual fiber optics for reflected illumination. It is equipped with a color CCD camera connected to the ProgRes C14 acquisition software. A choice of filter cubes is available for fluorescence imaging:

Filter Cube UV (DAPI)
  • Excitation filter: 350/50
  • Emission filter: 460/50
Filter Cube BP Green (FITC)
  • Excitation filter: 480/30
  • Emission filter: 535/40
Filter Cube LP Green (GFP)
  • Excitation filter: 470/40
  • Emission filter: LP 500
Filter Cube Red (TRITC)
  • Excitation filter: 540/25
  • Emission filter: 605/55

This scope can be used free of charge following a free fifteen-minute training.

Training is required.

Leica DM5500 Epifluorescence Microscope is equipped with five objectives: 10X dry, 20X immersion, 40X dry, 63X water, and 63X oil. All objectives are equipped for bright field and Polarized imaging. DIC is currently unavailable on 10X and 40X. It has an automatic touch pad for lowering and raising the stage. A choice of filter cubes is available for fluorescence imaging. It is equipped with a color CCD camera Retiga-2000R connected to the Qcapture Pro 6.0 acquisition software.

Filter Cube UV A
  • Excitation filter: BP 340-380
  • Dichroic mirror: 400
  • Emission filter: LP 425
Filter Cube Green 13
  • Excitation filter: BP 450-490
  • Dichroic mirror: 510
  • Emission filter: LP 515
Filter Cube Green (GFP)
  • Excitation filter: BP 450-490
  • Dichroic mirror: 500
  • Emission filter: BP 500-550
Filter Cube Red N2,1
  • Excitation filter: BP 515-560
  • Dichroic mirror: 580
  • Emission filter: LP 590

This scope can be used free of charge following a free thirty-minute training.

Our free training covers all the basics of the microscope and image acquisition. Training takes about thirty minutes, and you can take it any day between 9 am and 1 pm (except Thursdays). Contact PCIC in advance to make sure that we are available to provide the training.

After an initial training, all instruments can be scheduled through the shared Microsoft Calendar.

To schedule an appointment for training with microscope use, or for questions, please contact us or call (607) 254-4436 between the hours of 9 am and 1 pm.

Olympus SZX12 Stereomicroscope

There is no usage charge for this microscope. Training is free.

Our free training covers all the basics of the microscope and image acquisition. Training takes about thirty minutes, and you can take it any day between 9 am and 1 pm (except Thursdays). Contact PCIC in advance to make sure that we are available to provide the training.

Leica DM5500 Epifluorescence Microscope

There is no usage charge for this microscope. Training is free.

Our free training covers all the basics of the microscope and image acquisition. Training is about thirty minutes, and you can take it any day between 9 am and 1 pm (except Thursdays). Contact PCIC in advance to make sure that we are available to provide the training.

Leica TCS SP5 Confocal Microscope

The hourly fee for the confocal microscope is $28.50 an hour. The training fee is $110 (approx. 2.5-3.0 hours general training).

The three-hour training session covers all the basics of the microscope and its software. If needed, we can tailor the training to specific areas of interest. Training is typically provided to up to three people at a time, and users do not need to bring samples.

After training is completed, free assistance is available during the following times:
– Monday (all day)
– Wednesday (9:00 AM–1:00 PM)
– Friday (all day)

To schedule a session, please contact pcic@cornell.edu. Note: A completed Confocal Authorization Form must be submitted at least 24 hours before the training session.

Get in touch

Don't hesitate to reach out with any questions about the PCIC facility, its equipment, or our services.

Mailing Address

Mamta Srivastava, PhD
Manager, Plant Cell Imaging Center
Boyce Thompson Institute
533 Tower Road
Ithaca, NY 14853-1801

E-mail List
Listserv Info

The PCIC Listserv allows its members to receive updates regarding our facility and to share information. It is also the place where confocal users will post reservation changes or cancellations. For this reason, all confocal users are automatically subscribed after training (unless specifically requested). Once subscribed to this list, you can send a message to all its members. Messages sent to this list are not edited or moderated, and should be restricted to PCIC or microscopy-related topics.