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Bio-Imaging Facility

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Lloyd Recent Zhong Wang

Director Dr. Lloyd Williams
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Office: 826B in the Hunter North Building
Phone: (212) 650 3872
Fax: (212) 650 3565

Assistant Zhong Wang
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Office: 826C in the Hunter North Building
Phone: (212) 396 6284
Fax: (212) 650 3565

Faculty Oversight
Prof. Diana Bratu
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NIH Logo NIoMHHD

Description of the Facility

Background Overview
The BioImaging Facility at Hunter College is centered in a multi-room facility of 1024 sq. ft. located in the Biological Sciences Department on the 9th Floor of Hunter North building. A satellite facility also includes a number of instruments on the 4th Floor of the Belfer Research building (at 69th Street and York Ave). Faculty and students have access to a broad spectrum of instruments, ranging from simple white light wide field microscopes to fluorescent multidimensional super-resolution and confocal imaging systems. The Faculty supervisor and Scientific Director is Dr. Diana P. Bratu. Dr. Lloyd Williams is the Managing Director of the facility who is assisted by a full time technician Mr. Zhong Wang. The facility staff has expertise in many areas of microscopy including the laser scanning confocal microscopy, super resolution microscopy, two-photon microscopy. They are also familiar with many image analysis software packages, including, Imaris, Volocity, Autoquant, MetaMorph and NIS-Elements. Detailed descriptions of the equipment in the facility is given below. All equipment is located at Rm 826 HN or at the 4th floor of the Belfer Research Building where designated

Instruments

Nikon TIRF SIM Scope Nikon Eclipse Ti, TIRF/SIM
The Nikon TIRF SIM microscope allows the users to do both Total Internal Reflection Microscopy and SIM super-resolution microscopy. The acquisition software is Nikon elements.
The charge for this instrument is $20/hr.
To book time, use the SharePoint Calendar at
http://biosharepoint.hunter.cuny.edu/Bio-Imaging/Lists/TIRF%20SIM%20Calendar/calendar.aspx
Nikon A1 Confocal Microscope Belfer Nikon A1 Confocal Microscope
The Nikon A1 Confocal microscope is Nikon's powerful fully-automated confocal imaging system, capable of capturing high-quality confocal images of cells and molecular events at high speed and enhanced sensitivity. The acquisition software is Nikon elements. The system is located at Belfer Research Building. 
The charge for this instrument is $20/hr.
To book time use the SharePoint Calendar at
http://biosharepoint.hunter.cuny.edu/Bio-Imaging/Lists/Nikon%20A1%20confocal%20microscope%20Belfer%20Building/calendar.aspx
NikonDG5Scope Nikon Eclipse Ti Mosaic/MicroPoint System & FRAP
The Nikon Eclipse Ti scope is a wide-field fluorescent microscope. It is equipped with Andor iXon EMCCD camera, and a DG5 wavelength switcher. It is also equipped with an Andor Mosaic/MicroPoint system for Optogenetics, Opto physiology, photobleaching/activation and uncaging applications
The charge for this instrument is $15/hr.
To book time on this system use the Sharepoint Calendar at
http://biosharepoint.hunter.cuny.edu/Bio-Imaging/Lists/Nikon%20Eclipse%20Ti%20With%20Ultra%20High%20Speed%20Wavelength/calendar.aspx
PE UltraView Perkin Elmer UltraView ERS
The UltraView is a spinning disk confocal microscope equipped with six laser lines, which allow visualization of GFP, RFP, CY5, DAPI, CFP and YFP, etc. The UltraView ERS system allows for high-speed, multiple-probe, time-lapse experiments; Volocity 3D Image analysis software is used for image acquisition and analysis.
The charge for this instrument is $20/hr.
To book time on this system use the SharePoint Calendar at http://biosharepoint.hunter.cuny.edu/Bio-Imaging/Lists/Spinning%20Disk%20Calendar/calendar.aspx
Leica Confocal Leica Confocal Microscope TCS SP2
The TCS SP2 Laser Scanning Spectral Confocal Microscope can do measurements of transmitted light, fluorescence and laser scanning fluorescence imaging.
The charge for this instrument is $20/hr.
To book time on this system use the SharePoint Calendar at
http://biosharepoint.hunter.cuny.edu/Bio-Imaging/Lists/Leica%20Confocal%20Calendar/calendar.aspx
Calcium Ratio Scope Nikon Eclipse TE 200 Calcium Ratio & Micro Injection  
The calcium ratio imaging system consists of: a Nikon Eclipse TE 200 inverted epifluorescence microscope, Sutter Lambda 10-2 optical filter system, and Nikon NIS Elements imaging software with Calcium & FRET plug-in. The system also is equipped with a Narishige micromanipulator system.
The charge for this instrument is $10/hr.
To book time on this system use the Calcium Imager SharePoint Calendar at
http://biosharepoint.hunter.cuny.edu/Bio-Imaging/Lists/Calcium%20Imager%20Calendar/calendar.aspx
Belfer Nikon Ti-S Flourescence Microscope Belfer Nikon Ti-S Flourescence Microscope
The Nikon Ti-S microscope has a SOLA Light Engine solid state light source and a Nikon DigiSight camera. It has filter sets for DAPI FITC and RFP
The charge for this instrument is $10/hr.
JEOL TEM JEOL JEM-100C/CX Transmission Electron Microscope
JEOL JEM-100CX II transmission electron microscope is an advanced high-performance electron microscope with stable and excellent imaging capabilities at low to high magnifications (90X to 800, 000X). A 10M-pixel HAMAMASTU C4742-95 digital camera is integrated into the system for high-resolution image acquisition.
Nikon E400 Nikon Eclipse E 400  Color Image Analysis System
The Nikon Color Imaging system consists of a Nikon Eclipse E400  upright microscope, and Nikon DXM 1200F high-resolution (3,840 x 3,072 pixels) color video camera. The microscope is equipped for fluorescence and has phase contrast and Nomarski optics. The system is interfaced to a 1.4Ghz PC which utilizes Nikon Imaging Software. The system also has Adobe Photoshop installed for image acquisition and manipulation
The charge for this instrument is $5/hr.
BitPlane Imaris Imaris Imaging Station
The Imaris Imaging station is a high-power workstation with Bitplane's Imaris Imaging software installed. Imaris provides functionality for the visualization, segmentation, and interpretation of 3D and 4D microscopy datasets.
the charge for this instrument is $10/hr.
To book time on this system use the Imaris SharePoint Calendar at
http://biosharepoint.hunter.cuny.edu/Bio-Imaging/Lists/Imaris%20Calendar/calendar.aspx
NIS Elements NIS-Elements Imaging Station
This Imaging worksttion is a high-power workstations with Nikon's NIS-Elements Imaging software installed. NIS-Elements provides cutting edges tools for image manipulation and data management.
The charge for these instruments is $10/hr.
To book time on these systems use the Bioimaging SharePoint Calendar at:
http://biosharepoint.hunter.cuny.edu/Bio-Imaging/Lists/NIS%20Elements%20Calendar/calendar.aspx
AutoQuant Autoquant and NIS-Elements Imaging Analysis Station
This Imaging workstion has both AutoQuant and Nikon's NIS-Elements Imaging software installed.
AutoQuant is used to deconvolve images aquired in the facility
The charge for this instruments is $10/hr.
To book time on these systems use the Bioimaging SharePoint Calendar at:
http://biosharepoint.hunter.cuny.edu/Bio-Imaging/Lists/Drobo_PC%20NIS%20Elements%20Calendar/calendar.aspx
Belfer Analysis Belfer NIS-Elements Deconvolution Analysis Station
This Imaging workstion has Nikon's NIS-Elements Imaging software installed. Additionally it has Elements deconvolution module installed.
The charge for this instruments is $10/hr.
Gemini EM Gemini EM Microplate Spectrofluorometer
The Molecular Devices SpectraMax Gemini EM Microplate Spectrofluorometer features top and bottom reading optics, dual monochromators, wavelength scanning, well scanning, auto PMT gain and is driven by Softmax Pro software on a Windows-based controller.
The charge for this instrument is $5/scan
Typhoon 9410 Amersham Biosciences Typhoon 9410
Typhoon is a highly sensitive variable-mode gel imager. The Typhoon 9410 unites the ability to detect an extensive variety of fluors, with proven storage phosphor autoradiography technology and direct imaging of chemiluminescence. The typhoon can also be used to analyze microarrays.
The charge for this instrument is $5/scan
Belfer GE FLA 7000 Belfer GE FLA 7000 Typhoon
Typhoon FLA 7000 is a fast laser scanner for biomolecular imaging applications including sensitive and quantitative measurements of radioisotopic labels, chemifluorescent Western blots, and single fluorescence.
The charge for this instrument is $5/scan
Odyssey Infrared Imager Odyssey Infrared Imager
The Odyssey replaces the tradition methods of analyzing western blots,  chemiluminescence, and fluorescence detection, with near-infrared (NIR)   fluorescence detection.  This allows you to quantitate proteins over a much wider linear dynamic range than chemiluminescence can. This feature can enable strong and weak bands on the same blot to be accurately quantified without the need for multiple exposures.  In addition, the Odyssey is uniquely equipped with two infrared channels 700 nm and 800 nm, and can thus probe two different targets in the same experiment.
The charge for this instrument is $5/scan
PowerWaveHT Microplate PowerWave HT Microplate Spectrophotometer
PowerWave HT is a multi-channel reader for maximum speed in both 96- and 384-well plate formats. The PowerWave HT provides flexibility for multiple applications, including endpoint, kinetic and spectral scanning mode. Powerful Gen5 PC-based software is used for system control and data analysis.
The charge for this instrument is $3/scan
Belfer Bio Tek Synergy HTX  Microplate Reader Belfer Bio Tek Synergy HTX Microplate Reader
Synergy HTX is a Multi-Mode Microplate Reader for making: absorbance, fluorescence, luminescence and AlphaScreen/AlphaLISA measurements on 6- to 384-well microplates.
The charge for this instrument is $3/scan
GloMax Luminometer GloMax®-96 Microplate Luminometer The GloMax®-96 Microplate Luminometer is a state-of-the-art Microplate Luminometer with a high sensitivity and broad dynamic range that is necessary for chemiluminescent and bioluminescent applications. The GloMax uses an advanced photon-counting photomultiplier tube (PMT), with a dynamic range of greater than nine logs. This range covers virtually all chemiluminescent and bioluminescent assays, eliminating the need to dilute samples or manage detector-driven gain changes.
The charge for this instrument is $5/scan
Leica Cryostat1 Leica CM 3050S Cryostat
The Leica CM 3050S Cryostat features motorized sectioning and programmable defrost cycles. The cryostat can cut sections in the range  0.5 to 300 mm. The max specimen size is 55 X 70 mm and can cool samples down to - 50°C.
The charge for this instrument is $5/hr. Sign the log book when you use this system 
To book time on this system use the Cryostat SharePoint Calendar at
http://biosharepoint.hunter.cuny.edu/Bio-Imaging/Lists/Leica%20CM3050S%20Cryostat/calendar.aspx

Rules of Operations
Guidelines For using The Facility
A. The facility is open for use by members of the CTBR, other CUNY departments, and outside parties with the prior arrangement of the staff of the Bio-Imaging facility
B. Your use of the facility will be recorded. For the optical microscopes and the Gel and Blot scanners, you must obtain a "Gene Center" computer account. This is required to log on to the computers that control the equipment. Your use of the machine will then be automatically logged and you will be charged according to the fee schedule below.
C. The facility is available for use 7 X 24. After normal working hours ( 9-5 Mon-Fri ) lock the door when you leave, and access using a key obtained from the facility.
D. Training is required before using all machines. This can be done by individually with the facility manager, or by experienced users in the various CTBR laboratories. For the three confocals, and the Nikon SIM/TIRF  you must be trained by the facility managers. Once you have complete the training course your account will be activated for the microscope.

E. When using the Cryostat, sign the logbook.
F. If you encounter problems with the facility E-mail the facility director Lloyd Williams at This e-mail address is being protected from spambots. You need JavaScript enabled to view it ,  or his assistant Zhong Wang  at This e-mail address is being protected from spambots. You need JavaScript enabled to view it

G. Do not wear latex gloves in the facility
H. Do not leave your samples in the facility
I. Turn off all microscope lamps after use. It is particularly important to turn off the mercury lamps. Once mercury lamps have been turned off do not turn them back on until they have cooled down for 15 minutes
J. Report mercury lamps in service for more than 300 hours
K. Equipment is available on a first come first serve basis.  You can book 4 hours slots on the microscopes using the facility's SharePoint Site: https://biosharepoint.hunter.cuny.edu/Bio-Imaging. If you come 30 minutes late you will lose your reservation. You will need a "Gene Center" network account to access the site. 
L. Users may have no more than 2 reservations made on a calendar at one time for any single machine.
For example, Monday 12-4pm, Tues 9-1pm. After Monday's session, the user may schedule another session, thus obtaining another/2nd appointment on the calendar, say Wed 2-5pm.
M. Clean oil off the microscope objective lenses after use.
N. Report all accidents (injuries, spills, fires) to the Security (x4444) and Health and Safety Officer, Ricardo Franco (x4462)
O. You must log in to use the equipment using your own Gene Center account.
P. Publications using data taken in this facility must acknowledge the RCMI program and the NCRR. Suggested language for the acknowledgment would be,

"This project was supported by a Research Centers in Minority Institutions Program grant from the National Institute on Minority Health and Health Disparities (MD007599) of the National Institutes of Health."

Fee Schedule

PerkinElmer Spinning Disk Microscope:
The facility charges $20 per hour for use of this microscope. There is a $20 minimum charge, and fractions of an hour count as whole hours. For long time duration experiment, we have a special rate policy described as follows: in any 24 hour period
0 - 4 hours $20/hour
4 - 10 hours $10/hour
10 - 24 hours $5/hour
Email Zhong Wang ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ) in advance for applying this policy.
Leica Sp2 Confocal: The facility charges $20 per hour for use of the confocal. There is a $15 minimum charge, and fractions of an hour count as whole hours.
Nikon SIM/TIRF: The facility charges $20 per hour for use of this microscope. There is a $15 minimum charge, and fractions of an hour count as whole hours.
Nikon Eclipse Ti With Ultra High-Speed Wavelength Source: The facility charges $15 per hour for use of this microscope. There is a $15 minimum charge, and fractions of an hour count as whole hours.
All Other Nikon Upright & Inverted Microscopes: The facility charges $10 per hour for use of the microscope. There is a $10 minimum charge, and fractions of an hour count as whole hours.
Leica CM 3050S Cryostat: The facility charges $5 per hour for use of the Cryostat. There is a $5 minimum charge, and fractions of an hour count as whole hours. Please sign the log book.
Gemini Spectrophotometer, Typhoon 9410 Imager: The facility charges $5 per scan. Use is monitored by the event log on the computer attached to the machines.
PowerWave HT Plate Reader: The facility charges $3 per scan. Use is monitored by the event log on the computer attached to the machines.
Elements Analysis Workstation: The facility charges $10 per hour for use of this image analysis package. There is a $10 minimum charge, and fractions of an hour count as whole hours.
Volocity Analysis Workstation: The facility charges $10 per hour for use of this image analysis package. There is a $10 minimum charge, and fractions of an hour count as whole hours.
Imaris Analysis Workstation: The facility charges $10 per hour for use of this image analysis package. There is a $10 minimum charge, and fractions of an hour count as whole hours.

Remote Instrumentation

Purpose
Nowadays, microscopic imaging techniques are becoming more and more popular in biomedical research.   Most of the advanced high-end microscope systems (i.e., confocal & spinning disk systems) are expensive, not every research lab can have enough fund to support such system for their research.  A solution to overcome this problem is to share the microscope systems through Internet (also called remote instrumentation): remote users can get the control of the microscope for their experiment through a simple Internet connection. Our approach for this remote instrumentation task is to combine the powers of WebEx and PVX:
(i) Utilize WebEx to setup remote desktop sharing for microscope control.
(ii) Utilize PVX monitoring system to setup Internet video conferencing for remote communication purpose.
Remote instrumentation service
Now a new service is ready for our remote users to get remote access to our advanced confocal microscopes for their own imaging purpose.
 Our service includes:
(i) Leica SP2 confocal microscope: it is ideal for regular 2D & 3D scanning for fixed slide samples.  Please check the following link for  Leica SP2  system:  Leica SP2 operational guide;
(ii) Perkin Elmer spinning disk microscope:  besides the regular 2D & 3D fixed slide scanning, it is also equipped with an environment chamber for live cell imaging. Also, this type of microscope system has fast scanning speed, it is ideal for cellular dynamic studies.  Please check the following link for  Perkin Elmer spinning disk microscope system:  Spinning disk operational guide;
(iii)  Microscope remote control: Webex is used to setup the remote desktop sharing for microscope control. Please check the following link for  WebEx-based remote control operations:  Webex remote control  guide;
(iv) PVX video conferencing for real-time consultation: during imaging experiment,   PVX video conferencing system is used for real-time conversations between microscope operator and remote users to solve on-site experimental issues. Please check the following link for PVX real-time conferencing:  PVX video conferencing operational guide.
(v) Cell staining protocol:  a simple cell staining protocol is posted here as an example: Sample staining protocol.

For scheduling the above remote instrumentation service, please check the following guidelines: 

  1. Contact us by email for scheduling a remote microscopic imaging experiment, including, a short description of your experiment, time schedule, sample type, etc.
    Contact emails:
    • Zhong Wang: This e-mail address is being protected from spambots. You need JavaScript enabled to view it
    • Dr. Lloyd Williams: This e-mail address is being protected from spambots. You need JavaScript enabled to view it
  2. Ship the sample slide or living samples with proper package.
  3. A confirmation email will be sent before the experiment date.  A WebEx meeting link will be included in this email for remote connection.

 

Application Summary for Different Readers in Bio-Imaging Facility

 Glomax 96
Microplate
Luminometer
Biotek PowerWave
HT Plate Reader
SpectraMax
Gemini EM
Fluorescence Spectrometer
Typhoon 9410 ImagerLI-COR Odyssey
Sample Type 96-well plate 96 & 384-well plate 96 to 384-well plate Plate/Gel/Blot Western blot sample
Excitation
Wavelength
Range
N/A 200-999nm 250-850nm 457nm/488nm/
532nm/633nm
680nm/780nm
Detection
Wavelength
Range
300-650nm 200-999nm 360-850nm 500-685nm Near-infrared detection 680-1000nm
Detection Mode Luminescence Absorbance Fluorescence Phosphorimaging Chemiluminescence Fluorescence Fluorescence
Read Mode Endpoint/Kinetics Endpoint/Kinetics Endpoint/Kinetics
/Spectrum
Image Image
Application Chemiluminescence Bioluminescent assay Direct DNA quantitation Purity testing
RNA quantitation
ELISA Enzyme Kinetics
Colorimetric assays
ELISAs and Immunoassays
Nucleic Acid Quantitation
Protein Quantitation
Reporter Gene Assays
Cell Viability,
Proliferation, and Cytotoxicity Enzyme Assays
Transporter Assays Phosphatases/Kinases Microbial Growth
Quantitative Phosphorimaging ECL Plus Westerns Multifluorescence applications (such as 2-D DIGE and ECL Plex) Quantitative Western
ELISA/FLISA
In-cell Western Assay
In-Gel Western Assay
On-cell Western Assay
Microwestern

 

 

Objectives of Microscopes in the Bio-imaging Facility

Lens\System Nikon Upright Nikon Inverted Leica Confocal PE Spinning-disk Nikon TIRF/SIM
Objective
Description
Magnification/NA
/Immersion (dry lens unless mentioned)
4x/0.13 4x/0.1 5x/0.15 20x/0.75/multi 40x/0.6
10x/0.45 10x/0.3 10x/0.4 60x/1.4/oil 60x/1.49/oil
20x/0.75 20x/0.45 20x/0.5 100x/1.4/oil 100x/1.49/oil
40x/1.0/oil 40x/0.6 40x/1.25/oil
60x/1.4/oil 63x/1.4/oil
100x/1.4/oil

 

Laser wavelength specifications for various instruments

Leica SP2 Confocal, Room 826 HN

Argon Ion Laser

458, 476, 488, 514 nm

Melles Griot Solid State Laser

561 nm

HeNe Laser

633 nm

PE Spinning-disk Room 826 HN

Solid State Laser

561 nm

Solid State Laser

405 nm

Solid State Laser

488 nm

Solid State Laser

514 nm

Solid State Laser

440 nm

Solid State Laser

640 nm

Nikon TIRF/SIM Room 826 HN

TIRF Module

 

Solid State Laser

405 nm

Solid State Laser

488 nm

Solid State Laser

561 nm

Solid State Laser

640 nm

SIM module

 

Solid State Laser

488 nm

Solid State Laser

561 nm

Solid State Laser

640 nm

Nikon Eclipse Ti Mosaic/MicroPoint System & FRAP Room 826 HN

Solid State Laser

405 nm

Amersham Biosciences Typhoon 9410 Room 826 HN

Argon Ion Laser

457, 488 nm

SYAG laser

561 nm

HeNe Laser

640 nm

Nikon A1R Resonant Confocal ( Room Belfer BB 453).

Solid State Laser

405 nm

Solid State Laser

488 nm

Solid State Laser

561 nm

Solid State Laser

640 nm

GE FLA 7000 Typhoon (Room Belfer BB )

Solid State Laser

473 nm

Solid State Laser

532 nm

Solid State Laser

635 nm

Solid State Laser

650 nm


Website:
Biology Department

The Digital Bio-Imaging Facility is supported by a Research Centers in Minority Institutions Program grant from the National Institute on Minority Health and Health Disparities (MD007599) of the National Institutes of Health.

 

Last Updated ( Wednesday, 08 March 2017 17:46 )