Biology

Director Dr. Lloyd Williams Email: This e-mail address is being protected from spambots. You need JavaScript enabled to view it Office: 826B in the Hunter North Building Phone: (212) 650 3872 Fax: (212) 650 3565	AssistantZhong wang Email: This e-mail address is being protected from spambots. You need JavaScript enabled to view it Office: 826C in the Hunter North Building Phone: (212) 396 6284 Fax: (212) 650 3565
Faculty Oversight Prof. Jason Dictenberg Email: This e-mail address is being protected from spambots. You need JavaScript enabled to view it	Faculty Oversight Prof. Diana Bratu Email: This e-mail address is being protected from spambots. You need JavaScript enabled to view it

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 equiped with two confocal miroscopes, 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 addtion to the afore mentioned scopes the facility is also equipped for bright field, phase contrast, modulation contrast and epi fluorescence 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 Meta Fluor software. The facility also has two powerful imaging workstations equiped with Nikon Elements and BitPlane Imaris for Image analysis.  The facility has recently expanded with the aquisition of a JEOL JEM-100C/CX Transmission Electron Microscope.The facility also is equiped with Typhoon 9410 scannerf or 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 desciptions of the facilities equipment is given below.

Instruments

	Nikon TIRF/SIM Microscope The Nikon TIRF SIM microscope allows the users to do both Total Internal Reflection Microscopy and SIM super reolution microscopy. The acquisition software is Nikon elements. To book time use the SharePoint Calandar at https://biosharepoint.hunter.cuny.edu/Bio-Imaging/Lists/TIRFSIM%20Calandar/calendar.aspx
	Imaris Imaging Station The Imaris Imaging station is a highpower worksation with Bitplane's Imaris Imaging software installed. Imaris provides functionality for the visualization, segmentation and interpretation of 3D and 4D microscopy datasets. To book time on this system use the Imaris Sharepoint Calander at https://biosharepoint.hunter.cuny.edu/Bio-Imaging/Lists/Imaris%20Calander/calendar.aspx
	NIS Elements Imaging Station The NIS Elements station is a highpower worksation with Nikons 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 Calander at https://biosharepoint.hunter.cuny.edu/Bio-Imaging/Lists/NIS%20Elements%20Calandar/calendar.aspx
	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
	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.
	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; fully automated image capture; time-lapse morphometric measurements; fast sequential image capture of multiple probes; and fast z-stack acquisition. UltraVIEW ERS Imaging Suite software and Volocity are used for fast image display, image acquisition and comprehensive image analysis. The system is supported by a Nikon Eclipse TE2000 inverted fluorescence microscope with environmental incubator which is ideal for live cell applications. To book time on this system use the Spinning D isk Sharepoint Calander at https://biosharepoint.hunter.cuny.edu/Bio-Imaging/Lists/Spinning%20Disk/calendar.aspx
	Odyssey Infrared Imager The Odyssey  replaces the tradition methods of analysing 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 acurately quantified with out 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.
	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.
	Compix Color Image Analysis System The Compix 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 Compix Simple PCI image analysis software. The system also has Adobe Photoshop installed for image acquisition and manipulation Rate: The facility charges $5:00 per hour to use this system
	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.
	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. It has a z-stage with rotation capabilities, with z-resolution of 40 nm. The system has high quality X10, X40, X63 and X100 objectives, and 6 excitation laser lines at wavelenghts of 458nm - 638 nm. Cost to use this instrument is $15/hr To book time on this system use the Spinning D isk Sharepoint Calander at https://biosharepoint.hunter.cuny.edu/Bio-Imaging/Lists/Leica%20SP2%20Confocal/calendar.aspx20Disk/calendar.aspx
	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. To book time on this system use the Calcium Imager Sharepoint Calander at https://biosharepoint.hunter.cuny.edu/Bio-Imaging/Lists/Calcium%20Imager%20Calendar/calendar.aspx
	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.

Rules of operations
Guidelines For using The Facility
A. The facility is open for use by members of the Gene Center, 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 gene center laboratories. For the two confocals you must be trained by the facility managers. Once you have complete the traing 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 mins
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, Ricarod 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 acknowlege the RCMI program and the NCRR. Suggested language for the acknowlegement would be,

“This project was supported by grants from the National Center for Research Resources (G12 RR003037) and the National Institute on Minority Health and Health Disparities (8 G12 MD007599) from 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 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. Please sign the log books.

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.

Densitometer, 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.

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

Objectives of Microscopes in the Bioimaging Facility

Laser wavelength specifications for Leica SP2 Confocal and PerkinElmer SpinningDisk Microscope

Website:
Biology Department

This facility is supported and funded by the Research Centers in Minority Institutions Program, Division of Research
Infrastructure, National Center for Research Resources, and the National Institutes of Health.