Laboratory for Fluorescence Dynamics

Laboratory for Fluorescence Dynamics
A national research center for biomedical fluorescence spectroscopy at the University of California, Irvine

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Resources and Facilities

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

Microscopy

As of April 2019.

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 Globals for Images software:

  1. M1: Olympus IX81 microscope with Spectra-Physics MaiTai HP laser for GP, FCS, and FLIM.
  2. M3: Zeiss Axiovert S100TV microscope with with Spectra-Physics MaiTai HP laser (shared with M2) and Becker & Hickel SPC-830 card for FLIM.
  3. M5: Olympus IX70 microscope with Coherent Chameleon-Ultra II laser for 3D tracking.
  4. DIVER: Olympus BX & LCPlanFl microscope with Spectra-Physics MaiTai HP deapsea 680-1300nm laser and large area detector efor deep tissue imaging.

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

  1. LSM880: Zeiss LSM880 NLO with AiryScan.
  2. LSM710: Zeiss LSM710 system with AXIO Observer Z1 microscope and spectral detectors.
  3. STED: ISS Alba STED confocal lifetime imaging system with FLIM and Nikon Eclipse TE2000-U microscope.
  4. OLYMPUS: Olympus FluoView FV1000 system with IX81 microscope.

Camera based microscopes:

  1. TIRF2: Olympus IX83 microscope with two Photometrics 95B sCMOS cameras for 4-channel imaging.
  2. TIRF: Olympus IX81 microscope with TIRFM illuminator and objectives, with LI2Cam, pco.flim, and Evolve cameras, and multiple light sources (405, 458, 488, 515, 544, and 594 nm).
  3. uSPIM: custom body, Andor Zyla sCMOS cameras.
  4. SPIM: custom body, Photmetrics Prime 95B and pco.edge sCMOS cameras.

Four more microscopes are available to LFD users athe the Digman lab:

  1. ZEISS: Zeiss LSM 510 META-Confocor 3 (one-photon) system with Axiovert 200M microscope.
  2. KECK1: Olympus FV1000, SIM scanner, DIVER
  3. KECK3: Olympus FV1000 upright
  4. KECK4: Olympus FV1000, spectral imaging

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

Spectroscopy

As of April 2019.

UV/Visible:

  1. PERKIN: Perkin-Elmer Lambda 40 spectrophotometer.
  2. SHIMADZU: SHIMADZU UV-1800

Steady-State Fluorescence:

  1. PC1: 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

As of October 2013.

  • 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

As of October 2013.

  • 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)

Machining Tools

As of June 2018.

  • MicroMill DSLS 3000 Desktop Machining System
  • Micro Lathe II - 4500
  • JET 6-Inch Industrial Bench Grinder
  • DEWALT DW872 14-Inch Multi-Cutter Saw
  • CRAFTSMAN 15" Drill Press

Computing Resources

As of October 2020.

The LFD maintains more than 60 computers and printers, a computer lab, dozens of networking services, and hundreds of software packages. The computing facilities are regularly used by more than 20 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

  • One Dell Precision 5820 workstation with 10 core CPU, 256 GB RAM, 4 TB NVMe SSD, 12 TB HDD, Windows 10 Pro Workstation 64-bit
  • 8 desktop computers with Windows 10 Pro 64-bit, 4-6 core CPU, 2 TB SSD, 16-64 GB RAM, and 24-32" monitors.
  • 70 TB of networked data storage space
  • Black and white Laser printer

Commercial Software

  • Globals for Images and Spectroscopy
  • GLOBALS UNLIMITED (DOS)
  • Microsoft Office 365 and 2019
  • MathWorks Matlab (4 licenses)
  • Adobe Creative Studio 5.5 (1 license)
  • Mercury Amira 4.1 (1 license, Legacy)
  • Microcal Origin 7.5 (5 licenses, Legacy)

Free or Open Source Software

  • Olympus FV10-ASW Viewer, Zeiss ZEN Lite, LSM Image Browser, NIS-Elements Viewer, Imaris Viewer, Leica LAS X
  • Fiji, ImageJ, ICY, QuPath, Orbit, CellProfiler, Cecognition, FlimFit, FluoRender, Voxx
  • ParaView, VisIt, Inviwo, MIPAV, MeVisLab, Slicer, MayaVi, VoreenVE
  • R, GnuPlot, Scilab
  • Chimera, VMD, PyMol, CueMol, RasMol, Mercury, ICM-Browser
  • OpenOffice, LibreOffice, Scribus
  • Firefox, Thunderbird, Chrome, Skype, FileZilla, WinSCP
  • GIMP, Paint.NET, Raw Therapee, IrfanView, Blender, POV-Ray, LibreCAD, Inkscape, XnView, Vips
  • VLC, VirtualDub, Audacity, HandBrake, Shotcut
  • Notepad++, Emacs, VIM, jEdit, Hex Edit
  • Visual Studio 2019 CE, Visual Studio Code, LLVM, Lazarus, Java SDK, NetBeans IDE, MSYS, PowerShell
  • Python (incl. Numpy, Scipy, matplotlib, IPython, Pandas, Jupyter Notebook, etc), WingIDE
  • TeXlive, MikTeX, LyX, TeXstudio, GhostScript
  • ShareX, Zotero, and many more...

Legacy Hardware and Software

The LFD maintains one workstation with older hardware and software for compatibility with legacy files:

  • Fujitsu-Siemens Celsius R650, Xeon X5260 CPU, 12 GB RAM
  • ATI FireGL V5600 GPU
  • FireWire Port
  • Wacom tablet
  • Logitech QuickCam Pro 9000
  • CANON DR-1210C scanner
  • 3.5" floppy drive
  • Iomega Zip 100 and 250 drives available on demand
  • Windows 7 Pro SP1
  • GLOBALS UNLIMITED 1.2
  • Windows MovieMaker 2012
  • Microsoft Office Pro 2010
  • Adobe CS3
  • Acrobat Pro 8.3
  • Adobe PageMaker 9.5
  • Aldus PageMaker 6.5
  • Apple QuickTime Pro 7.7
  • FileMaker Pro Advanced 8
  • Camtasia Studio 6
  • TechSmith Snagit 9
  • ACD Canvas 9
  • MetaTools Soap
  • BobCAD-CAM V21
  • Jasc PaintShop Pro 9
  • Jasc Animation Shop 3
  • Endnote X
  • Visual Studio Pro 2008 and 2010
  • CANON CapturePerfect 3
  • ScanSoft OmniPage SE 4
  • Becker&Hickl SPCImage 5.3
  • TrueCrypt 7.1a
  • Synergy KaleidaGraph 3.5
  • WaveMetrics Igor Pro 5.0
  • Fortner Noesys 2.0
  • Fortner Plot, Transform, and Slicer
  • Visual Numerics PV-Wave 6.2 (no longer working)

Laboratory for Fluorescence Dynamics.  University of California, Irvine.  Department of Biomedical Engineering.  3208 Natural Sciences II.  Irvine, CA 92697‑2715, USA.  Phone: +1‑949‑824‑7085.  Email: lfd@uci.edu.  Copyright © 2006‑2023.