Resources and Facilities

As of May 2008.

The Laboratory for Fluorescence Dynamics (LFD) maintains customized facilities for microscopy, spectroscopy, biochemistry, cell culture, and computing.

Microscopy

Many of the nine inverted microscopes can be used for multiple types of experiments such as GP, FCS, FLIM, RICS, N&B and particle tracking. A detailed description of the instruments is available.

Five highly customized 2-photon laser scanning microscopes are controlled by SimFCS software developed at the LFD:

1. M1: Zeiss Axiovert 35 microscope with Coherent Verdi-V5 and Mira 900 lasers and mirror scanner.
2. M2 (not in service): Zeiss Axiovert 135TV microscope with Coherent Verdi-V5 and Mira 900 lasers and piezo stage scanner.
3. M3: Zeiss Axiovert S100TV microscope with Spectra-Physics Mai Tai HP laser and mirror scanner.
4. M4: Nikon Eclipse TE300 microscope with Spectra-Physics Millennia and Tsunami lasers and piezo stage scanner.
5. M5: Olympus IX70 microscope with Coherent Chameleon-Ultra laser and and Cambridge Technologies mirror scanner.

Commercial one-photon confocal microscopes:

6. TIRF: Olympus IX81 microscope with TIRFM illuminator and objectives, two Photometrics Cascade EMCCD cameras, and multiple light sources (405, 458, 488, 515, 544, and 594 nm).
7. OLYMPUS: Olympus FluoView FV1000 confocal laser scanning microscope with FlimBox (at 443 nm).
8. ZEISS: Zeiss LSM 510 META-Confocor 3 laser scanning microscope with FlimBox (at 471 nm).

Commercial one and two-photon microscopes:

9. ALBA: ISS Alba FLIM confocal lifetime imaging instrument with Nikon Eclipse TE2000-U microscope and Spectra-Physics Millennia and Tsunami lasers.

Spectroscopy

UV/Visible:

1. LAMBDA: Perkin-Elmer Lambda 40 spectrophotometer.

Steady-State Fluorescence:

2. PC2: ISS PC1 photon counting spetrofluorimeter.
3. PC3: Horiba Jobin-Yvon FluoroMax-4 fluorimeter.

Time-Resolved Fluorescence:

4. L1: Custom multifrequency cross-correlation phase and modulation fluorometer based on ISS Koala automated sample compartment, modulatable LEDs (280, 295, 370, 405, 471, 443, and 630 nm), and modulatable Hamamatsu photomultiplier (up to 500 MHz).
5. L2: Custom time-domain, time correlated single photon counting fluorometer based on an ISS Koala automated sample compartment, Fianium Supercontinuum fiber laser (450-1900 nm, 19.5 MHz), Hamamatsu photomultiplier, and Becker & Hickl SPC-144 board.
6. L3 (not in service): Custom frequency-domain fluorometer based on ISS K2, Pockle cell modulator, and Xe lamp.

Biochemistry Resources

• Cold room
• Cryofreezer (-80°C)
• Chromatography area
• FPLC (Pharmacia)
• Electrophoresis (Pharmacia)
• Centrifuges (Beckman GPC & L8–70)
• pH meter
• pH-stat
• Analytical balance
• PhastSystem (Pharmacia)
• Lipid extruder (Lipex)
• Sonicator
• Wet chemistry benches
• Four fume hoods

Cell and Tissue Culture Resources

• Cell Culture Room (Biosafety Level 2) with 2 incubators and 2 laminar flow cabinets.
• 5 Incubation systems for microscopes, including 2x Harvard Apparatus, Bioptechs, Warner Instrumentation Corporation, and INU- Tokai-Hit (CO₂ controlled)

Computing Resources

The LFD maintains more than 50 computers and printers, a computer lab, dozens of networking services, and hundreds of software packages. The computing facilities are regularly used by more than 25 people. The computer lab, data acquisition computers, servers, and printers are networked via a 1 Gbps Ethernet and are organized in a Windows Active Directory. Detailed documentation is available at the LFD Internal Computing Web site.

Users of the LFD facilities will be provided with a user account and network connections for personal computers. The LFD does not provide any software for private computers.

Computer Lab

The computer lab provides facilities for data storage and backup, data analysis and visualization, multimedia creativity, office productivity, and software development. The facilities are available to all members and guests of the LFD.

Hardware

• Ten desktop computers operating under Windows Vista 64-bit.
• Two TB of networked data storage space with automated backup.
• Black and white Laser printer and color InkJet printer.
• Backup to LTO tape, CD and DVD media.
• Audio, image, and video acquisition and processing.

Commercial Software

• Globals for Images and Spectroscopy
• Microsoft Office 2007
• Microsoft Visual Studio 2008
• Adobe Acrobat 8
• Adobe Creative Studio 3.3
• Thomson Endnote X
• IDM UltraEdit 10
• Mercury Amira 4.1 (64 bit)
• Microcal Origin 7.5
• MathWorks Matlab 7.6 (64 bit)
• Wolfram Mathematica 6

Legacy software

• Wavemetrics Igor Pro 5
• Nero Burning ROM 7
• Macromedia Studio 8
• Camtasia Studio 2.1
• ACD Canvas X
• Visual Numerics PVWave 6.2
• Fortner Noesys 2.4

Free or Open Source Software

• OpenOffice
• ImageJ, MIPAV, MeVisLab, VisBio, Slicer, MayaVi, ParaView
• R, GnuPlot, Scilab
• VMD, PyMol, RasMol
• GIMP, Paint.NET, IrfanView, Blender, POV-Ray, OpenFDX
• VirtualDub, Audacity, VLC
• Emacs, VIM, jEdit
• Eclipse, Java SDK, MinGW
• Python (incl. wxPython, Numpy, Scipy, matplotlib, IPython), EPD, WingIDE 101
• MikTeX, WinEdit, LyX
• Cygwin
• many more...