Laboratory for Fluorescence Dynamics

A NIH research center for biomedical fluorescence spectroscopy at the University of California, Irvine

Notes

Resources and Facilities

As of October 2013.

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

Microscopy

Highly customized 2-photon laser scanning microscopes operating in non-descan mode are using FlimBox devices and Cambridge Technology mirror scanners, and are controlled by SimFCS software:

  1. M1: Olympus IX81 microscope with Spectra-Physics MaiTai HP laser for GP, FCS, and FLIM.
  2. M2: Zeiss Axiovert 135TV microscope with Spectra-Physics MaiTai HP laser for FLIM and 3D tracking.
  3. M3: Zeiss Axiovert S100TV microscope with with Spectra-Physics MaiTai HP laser (shared with M2) and Becker & Hickel SPC-830 card for FLIM.
  4. M5: Olympus IX70 microscope with Coherent Chameleon-Ultra II laser for 3D tracking.
  5. DIVER: Olympus microscope with Spectra-Physics MaiTai HP deapsea laser and large area detector for deep tissue imaging.

Commercial one/two-photon confocal laser scanning microscopes with added FlimBox devices and/or 3D tracking capabilities:

  1. ZEISS: Zeiss LSM 510 META-Confocor 3 (one-photon) system with Axiovert 200M microscope.
  2. OLYMPUS: Olympus FluoView FV1000 system with IX81 microscope.
  3. LSM710: Zeiss LSM710 system with AXIO Observer Z1 microscope and spectral detectors.
  4. ALBA: ISS Alba FLIM confocal lifetime imaging system with Nikon Eclipse TE2000-U microscope.

Camera based microscopes:

  1. TIRF: Olympus IX81 microscope with TIRFM illuminator and objectives, Photometrics Cascade EMCCD and Lambert Instruments LI2CAM ICCD cameras, and multiple light sources (405, 458, 488, 515, 544, and 594 nm).
  2. iSPIM: Olympus IX71 microscope with inclined selective plane illumination and Photometrics Evolve camera.

Note that many of the microscopes can be used for multiple types of experiments such as GP, FCS, FLIM, RICS, N&B and 3D tracking.

Spectroscopy

UV/Visible:

  1. PERKIN: Perkin-Elmer Lambda 40 spectrophotometer.

Steady-State Fluorescence:

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

Time-Resolved Fluorescence:

  1. 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), modulatable Hamamatsu photomultiplier (up to 500 MHz), and FlimBox device.
  2. BECKERHICKL: 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.

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

As of October 2014.

The LFD maintains more than 70 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 website.

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

Computer Lab

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

Hardware

  • 10 desktop computers with Windows 7 64-bit and 8 to 32 GB RAM.
  • 20 TB of networked data storage space with automated backup.
  • Black and white Laser printer.
  • Backup to CD and DVD media.
  • Audio, image, and video acquisition and processing.

Commercial Software

  • Globals for Images and Spectroscopy
  • Microsoft Office 2010
  • Microsoft Visual Studio 2010
  • Adobe Creative Studio 5.5 (1 license)
  • Mercury Amira 4.1 64 bit (1 license)
  • Microcal Origin 7.5 (5 licenses)
  • MathWorks Matlab 2014a 64 bit (4 licenses)
  • Wolfram Mathematica 9 (1 license)
  • Legacy: Microsoft Office 2007, Visual Studio 2008, Endnote X

Free or Open Source Software

  • Olympus FV10-ASW Viewer, Zeiss ZEN Lite, LSM Image Browser, NIS-Elements Viewer
  • Fiji, ImageJ, ICY, CellProfiler, Cecognition, FlimFit, FluoRender
  • ParaView, VisIt, MIPAV, MeVisLab, Slicer, MayaVi
  • R, GnuPlot, Scilab
  • Chimera, VMD, PyMol, RasMol, Mercury, ICM-Browser
  • OpenOffice, LibreOffice, Scribus
  • Firefox, Thunderbird, Chrome, Skype, FileZilla
  • GIMP, Paint.NET, IrfanView, Blender, POV-Ray, LibreCAD, Inkscape, XnView
  • VLC, VirtualDub, Audacity
  • Notepad++, Emacs, VIM, jEdit, Hex Edit
  • Lazarus, Eclipse, Java SDK, NetBeans IDE, MinGW, WinSDK
  • Python (incl. Numpy, Scipy, matplotlib, IPython, Pandas), WingIDE 101
  • MikTeX, WinEdit, LyX, GhostScript
  • CamStudio, ShareX, Zotero
  • and many more...