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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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Description of the Facility

Background Overview
The Bio-Imaging facility is located in room 826 of the North Building of Hunter College. The facility currently provides optical and video microscopy services.The facility is equipped with two confocal microscopes, a Leica TCS SP2, and a Perkin Elmer  UltraVIEW ERS Spinning Disc confocal. Recently we have added a Nikon SIM-TIRF super resolution microscope. In addition to the afore mentioned scopes the facility is also equipped for bright field, phase contrast, modulation contrast and epifluorescence microscopy. The facility has two separate wide field image analysis stations. A Nikon Optiphot microscope equipped with a color video system and Compix imaging software, and a Nikon Eclipse TE200 inverted scope. This inverted scope in specially configured to perform calcium ratio imaging is equipped with Molecular Devices MetaFluor software. The facility also has two powerful imaging workstations equipped with Nikon Elements and BitPlane Imaris for Image analysis.  The facility has recently expanded with the acquisition of a JEOL JEM-100C/CX Transmission Electron Microscope.The facility also is equipped with Typhoon 9410 scanner for the quantitation and localization of sub cellular fluorescent and radioactive molecules. In addition a Densitometer allows for the analysis of 1 and 2 D gels, Southern, northern and western blots and RFPL gels. The facility is also equipped with color and B&W  laser printers for the production of publication quality graphics  and presentation materials. Detailed descriptions of the facilities equipment is given below.

Instruments

Nikon TIRF SIM Scope Nikon TIRF/SIM Microscope
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 $15/hr.
To book time use the SharePoint Calendar at
http://biosharepoint.hunter.cuny.edu/Bio-Imaging/Lists/TIRF%20SIM%20Calendar/calendar.aspx
NikonDG5Scope Nikon Eclipse Ti With Ultra High Speed Wavelength Source
The Nikon Eclipse Ti scope is a wide field fluorescent microscope. It is equipped with Andor iXon EMCCD camera, and a Sutter Lambda DG5 wavelength switcher. It is also equipped with an Andor Mosaic/MicroPoint system for Optogenetics, optophysiology, photobleaching/activation and uncaging applications
the charge for this instrument is $15/hr.
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 Calender 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 $15/hr.
To book time on this system use the SharePoint Calender at
http://biosharepoint.hunter.cuny.edu/Bio-Imaging/Lists/Leica%20Confocal%20Calendar/calendar.aspx
Calcium Ratio Scope Calcium Ratio & Micro Injection Inverted Scope
The calcium ratio imaging system consists of: a Nikon Eclipse TE 200 inverted epifluorescence microscope, Sutter Lambda 10-2 optical filter system, and Molecular Devices imaging software MetaFluor. The system also is equipped with a Narishige micromanipulator system.
The charge for this instrument is $5/hr.
To book time on this system use the Calcium Imager SharePoint Calender at
http://biosharepoint.hunter.cuny.edu/Bio-Imaging/Lists/Calcium%20Imager%20Calendar/calendar.aspx
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 to the system for high-resolution image acquisition.
 Nikon Color Imaging Nikon Optiphot Color Image Analysis System
The Nikon Color Imaging system consists of a Nikon Optiphot 2 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 Calender at
http://biosharepoint.hunter.cuny.edu/Bio-Imaging/Lists/Imaris%20Calendar/calendar.aspx
NIS Elements NIS Elements Imaging Station
The NIS Elements station is a high-power workstation with Nikon's Imaging software installed. NIS Elements provides cutting edges tools for image manipulation and data management
To book time on this system use the Imaris SharePoint Calender at
http://biosharepoint.hunter.cuny.edu/Bio-Imaging/Lists/NIS%20Elements%20Calendar/calendar.aspx
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 Molecular Dynamics 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 micro-arrays.
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
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 two confocals you must be trained by the facility managers. Once you have complete the training course your account will be activated for the confocal.
E. 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
F. Do not wear latex gloves in the facility
G. Do not leave your samples in the facility
H. 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
I. Report mercury lamps in service for more than 300 hours
J. Equipment is available on a first come first serve basis. However you can book 2 hours slots on the microscopes Equipment is available on a first come first serve basis. However you can book 2 hours slots on the microscopes using the facilities SharePoint Site https://biosharepoint.hunter.cuny.edu/Bio-Imaging. If you come 30 minutes late you will loose your reservation. You will need a "Gene Center" network account to access the site If you come 30 minutes late you will loose your reservation
K. Clean oil off the microscope objective lenses after use.
L. Report all accidents (injuries, spills, fires) to the Security (x4444) and Health and Safety Officer, Ricardo Franco (x4462)
M You must log in to use the equipment using your own Gene Center account.
N 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 $15 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 $15 per hour for use of thi 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 thi 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 $5 per hour for use of the microscope. There is a $5 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.
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.
Printing: Inkjet usage is charged at 15 ¢/per page, color laser prints at 15 ¢/per page, black and white laser prints at 7 ¢/per page. Usage is monitored automatically by Print Manager Plus application.

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 Leica SP2 Confocal and PerkinElmer Spinning Disk Microscope

Laser\System

Leica SP2 Confocal

PE Spinning-disk

Nikon TIRF/SIM

Laser Line Description

Wavelength

Remark

Wavelength

Remark

TIRF Module

SIM Module

458nm

Argon Ion Laser

405nm

Solid State Laser

 405nm

 488nm

476nm

Argon Ion Laser

440nm

Solid State Laser

 488nm

 561nm

488nm

Argon Ion Laser

488nm

Melles Griot Argon Ion Laser

 561nm

 640nm

514nm

Argon Ion Laser

514nm

Melles Griot Argon Ion Laser

 640nm

 

561nm

Melles Griot Solid State Laser

568nm

Melles Griot Kypton Ion Laser

 

 

633nm

HeNe Laser

640nm

Solid State Laser

 

 

 

 

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, 17 December 2014 13:12 )