Cellular and Molecular Imaging Core

Location: FA 318 (door key access required) 

Two-photon microscopy has become an indispensable tool for cellular neuroscience, allowing high-resolution fluorescent imaging of cells in vitro and in vivo living brain and whole animals. The HyperScope system is a custom-build, two-photon microscope equipped with a Mai-Tai eHPDS broadly tunable Ti-sapphire laser (690-1040 nm), multiple objectives (16x, 20x and 40x), and stands on a Thorlabs breadboard and anti-vibration table. With the Scientifica SciCam Pro CCD camera, it is possible to perform functional imaging of video frame rates of 24 fps (full resolution) and 40 fps (binned 2 x 2). The detector assembly includes one red-shifted PMT and one GaAsP PMT modules, and epifluorescence imaging with filter sets for GFP (470/40x extinction, 525/50m emission) and mCherry (560/40x extinction, 630/75m emission). The scan mirrors in the imaging path can be arranged in multiple configurations depending on your needs. With up to 3 mirrors in series, you can choose between galvo/galvo (GG), resonant/galvo (RG), or resonant/galvo/galvo (RGG) arrangements. The microscope is fitted with an ultra-smooth Z-axis drive to ensure vibration free movement, with the Z-axis being controlled with software for acquiring z-stacks with a minimum step size of 0.1 mm. The addition of a Piezo z-axis objective positioner allows volume imaging up to 400 mm. The microscope can be easily configured and switched between in vitro and in vivo applications by removing the substage optics and riser block. The system is enclosed in a black-out cage to prevent light and noise pollution of biological samples.

This platform includes an award winning Scientifica SciScan acquisition software, allowing users to integrate SciScan easily with custom-written applications, such as LabView and ScanImage. The ScanImage software interface (Vidrio Technologies) used by Scientifica was developed by HHMI Janelia Farm specifically for neuroscience applications, and is considered to be the most advanced software for two-photon laser scanning on the market.

Key unique features of the Scientifica HyperScope include:

• SliceScope upright microscope with motorized frame sitting on top of a Thorlabs breadboard with tapped holes on top of a TMC Cleantop Optical Table
• Motorised positioning of objective and condenser in Z-axis, controlled by PatchPad
• Motorized Movable Base Plate for use with riser block and in vitro applications
• HyperScope Scan Path including up to three scanning mirrors
• HyperScope X-Galvo module
• HyerpScope Resonant X module (8 kHz resonant galvanometer)
• Pockel Cell (680-1100 nm) with 500:1 extinction ratio
• Workstation and data acquisition, which enables resonant imaging (with SciScan) and RG or RGG system for resonant and/or galvo imaging using ScanImage
• Detectors: 1 red-shifted PMT module, and 1 multi-photon GaAsP PMT module
• Objectives include: 16x (CFI75 LWD 16xW N.A. 0.80, W.D. 3.0 mm), 20x (XLUMPLFLM 20xW, N.A. 1.0, WD 2.0 mm, water immersion), 40x (LUMPPLFLN 40xW, N.A. 0.8, W.D. 3.3mm, water immersion)
• The system is compatible with RMS, M25, M27 and M32 threaded objectives allowing users to easily interchange objectives
• Filter sets: GFP (470/40x, 495LP, 525/50m), mCherry (560/40x, 585LP, 630/75m)
• SciCam Pro CCD camera with 24 fps at full resolution (40 fps binned 2 x 2)
• 15x eye-piece with FOV of 14.5mm and tiltable nose piece
• Piezo Objective Z-drive allows fast acquisition of volumes up to 400 microns travel for large and small objectives
• Laser: Mai-Tai eHP DS-244 Ti-sapphire oscillator (690 to 1040 nm, >2.4W average power, ~80 MHz repetition rate, <70 fs pulse width)

Location: FA 324

The Leica TCS SP8 LIGHTNING confocal allows image information extraction with super resolution acquisition that exploits the sub-diffraction lateral resolution of confocal microscopy. It allows to capture cellular details and observe dynamics with a resolution down to 120 nm, which is close to STED super resolution microscope capabilities. The upright confocal is capable of simultaneous collection from up to 3 detection channels (two PMTs, one HyD) using multiple laser lines (diode 405, blue 488, green 552, red 638 nm). The confocal is configured with a conventional tandem scanner (8 kHz), a super Z-galvo stage type S, multiple objectives (10x, 20x, 25x, 40x, 63x), and stands on an anti-vibration table. The confocal is connected to a computer workstation equipped with Leica LAS-X software and a 30 inch monitor.

Key features of the confocal include:

• DM 6000 upright with EL 6000 fluorescence
• Super Z Galvo stage, Type S
• Objectives: 10x (HC PL FLUOTAR 10x/0.30), 20x (HC PL APO 20x/0.7 IMM CORR CS2), 25x (HCX IRAPO L 25x/0.95 W 0.17), 40x (HC PL APO 40x/1.30 Oil CS2), 63x (HC PL APO 63x/1.40 Oil CS2)
• Filter sets:
• Tandem resonant scanner 8 kHz
• 2 PMT SP confocal detectors for imaging
• 1 HyD SP GaAsP detector for gated imaging
• Lasers: 405 nm DMOD Compact, Port UV/405, Blue 488 nm, Green 552 nm, Red 638 nm
• LAS-X navigator software
• LIGHTNING work station

Location: FA 324

THUNDER imagers are a brand-new class of computational clearing high-resolution wide-field microscopes developed exclusively by Leica Microsystems. These imagers can acquire sharp data and high-quality images by instant removal out-of-focus blur or haze inherent to thick 3D samples that are generally acquired using widefield microscopy. These imagers also significantly shorten the imaging workflow from image acquisition to data analysis with the new LAS-X navigator software. The THUNDER Imager 3D Tissue is a motorized upright microscope and is outfitted with a ultra-fast DFC 9000 GT/C camera, and is ideal for cell culture, tissues, fixed samples, and cleared tissues. The THUNDER Imager Model Organism is a M205 FCA stereomicroscope intended to image embryos, whole organs and small organisms.

Key features of the THUNDER 3D Tissue imager include:

• Objectives: 5x (HC PL FLUOTAR 5x/0.12), 10x (HC PL FLUOTAR 10x/0,32), 20x (HC PL FLUOTAR 20x/0.55), 63x (HC PL FLUOTAR 63x/1.30 oil)
• Scanning stage, DM4-6, 100x100, 2 mm
• Stage insert 2 slides 3”x2’, 76x52 mm
• Filter sets: GFP, RHOD, CY 5, and DAPI
• DFC 9000 GT/C Andor Zyla sCMOS camera
• 1 TB SSD RAID for LAS X workstation with 32” monitor

Key features of the THUNDER Model Organism imager include:

• Objectives: 1x (PLAN APO)
• XY-scanning stage 150x100 mm
• Handwheel-Motor Focus for M-series and foot switch
• Filter sets: GFP, TXR, CY 5 and DAPI
• DFC 9000 GT/C Andor Zyla sCMOS camera
• 1 TB SSD RAID for LAS X workstation with 32” monitor

Location: FA 312 (Shared Core/Equipment room, door code access required)

The Typhoon Phosphoimager is a fast and versatile laser scanner for sensitive and quantitative measurements of radio-isotropic-labeled samples. The Typhoon is a non-confocal variable mode laser scanner offering high-speed and resolution for precise quantitation of proteins, nucleic acids and other biomolecules. The scanner comprises "filmless" autoradiography with storage phosphor screens. The laser can generate 16-bit images at up to 25 μm pixel resolution to give precise quantitation in gels and blots, with a high speed to scan gels of up to 240 x 250 mm in less than 2 min. Two phosphor screens with a size of 200 X 250 mm are available for autoradiography. The scanner can detect a broad range of isotopes in radiolabeled samples. Directly adjacent to the phosphoimager system, there is a PC computer with a software package that allows on-site quantitative and qualitative analysis of images and data.

Key features of the Typhoon imager include:

• Applications: radioisotopic labels by storage phosphor, chemifluorescent Western blots, and single fluorescence, as well as digitization of colorimetric stains (e.g., Coomassie™ Blue and silver-stained gels)
• Resolution: 16-bit images are generated at up to 25 µm pixel resolution
• Speed: 24 x 25 cm gel can be scanned in less than two minutes at 100 µm resolution
• Four lasers: blue (473 nm), green (532 nm), red (635 nm), and red (650 nm)
• Radioisotopes: ³H,  ¹⁴C,  ³²P,  ³³P,  ³⁵S
• Max scanning area: phosphorimaging: 20 × 40 cm, fluorescence: 24 × 40 cm

Location: FA 312 (Shared Core/Equipment room, door code access required) 

The Biorad Chemidoc is an easy, high-performance gel and blot imaging for accurate quantification of protein samples in gels and membranes. The Chemidoc streamlines Western blotting in a five-step approach by combining traditional blotting techniques with innovative tools to allow improved band quantitation and quick assessment of electrophoresis results and blot transfer quality prior to western blotting. The Chemidoc enables rapid western blot results in as little as 15 min with efficient protein transfer in 3 min, and 5 min stain-free gel imaging. The imbeded software includes all the tools for quantitative and qualitative image and data analysis. Images taken on the ChemiDoc can also directly be print.

Key features of the ChemiDoc system include:

• Electrophoresis applications: protein including stain free and DNA gel imaging
• Blotting applications: identify and quantify proteins, DNA, protein-ligand interactions, etc. with chemiluminescence or colorimetric detection
• Internal computer with Image Lab Touch software
• Automatic recognition of application-specific tray and adjustment of imaging parameters and software options
• Illumination sources: Trans-UV, 302 nm excitation, Epi-white, Trans-white (requires White sample tray provided), Trans-blue 450-490 nm excitation (requires Blue sample tray provided)
• Detection: chemiluminescence filter 590/110 nm standard emission filter for protein and DNA gel and blot imaging.
• Detector: cooled CCD camera, 6 megapixels
• Exports data to a USB drive as SCN, TIFF, JPEG files

Location: FA 314 (Tissue Culture facility, door code access required)

The Trans-Blot Turbo transfer system combines traditional blotting techniques with modern filter paper and buffers allowing rapid transfer of proteins from gels to membranes with minimal preparation time. The system integrates a high amperage power supply that directs current between a built-in platinized titanium anode and a stainless steel cathode. 

Key features of the Turbo-Blotter include:

• Two cassettes with rapid transfer of 1-4 mini or 1-2 midi gels in 3 min in a single run

Location: FA 313 (Autoclave room)

The Integra media autoclave allows the rapid and gentle preparation of 1-10 liter culture medium. Precise controlling of temperature, time and pressure during the sterilization process guarantee constant high quality. The mediaclave can be used for the preparation and sterilization of numerous types of culture media, including media for C. elegans research. The wide adding port facilitates safe addition of supplements prior to dispensing. The mediaclave is connected to a peristaltic pump housed in a vertical flow workstation to fill petri dishes and vials. 

Key features of the Mediaclave include:

• Rapid and gentle preparation of 1-10 liter culture medium
• Large and strong magnetic stirrer with adjustable speed and reversing rotation direction ensures homogenous media preparation over a wide viscosity range
• Pt-1000 temperature probe and microprocessor control of process parameters.
• Fast heating and rapid cooling
• Peristaltic pump DOSE-IT housed in a AirClean vertical flow workstation can be used to fill containers of unusual volumes or shapes, i.e. petri dishes, bottles, flasks

Location: FA 312 (Shared Core/Equipment room, door code access required)

Two Biorad real-time PCR machines combine advanced optical technology with precise thermal control to deliver sensitive, reliable detection, quick set-up runs and monitoring of amplification traces in real-time on the integrated LCD touch screen. Directly adjacent to the two qPCR detection systems, there is a PC computer containing easy to use software for on-site analysis of qPCR data.

Key features of the CFX96 include:

• Up to 5-target multiplexing with sample volumes as low as 10 μl
• Thermal gradient feature
• Visualize all run data at once and export only the data you need in the format you want

Location: FA 312 (Shared Core/Equipment room, door code access required)

The QIAgility is a compact benchtop instrument that enables rapid, high-precision setup of PCR experiments with ready-to-use software for ease and convenience. The software provides step-by-step guidance for worktable setup and automatic calculation of all mixes, eliminating the need to program pipetting steps. Just select the kit and cycler, define your targets and start the run. For added flexibility the QIAgility is operated via a laptop computer.

Key features of the QIAgility include:

• Highly suited for laboratories performing PCR and RT-PCR reactions with applications in gene expression, cloning, genotyping and more
• The instrument uses 50 µl and 200 µl Conductive Filtered Tips for liquid-level sensing
• Accessories included: 2 x Adapter, 96 x 0.2 ml PCR Tubes 1 x Adapter, Flip-Cap 32 x 1.5 ml Tapered Base 1 x Adapter, 72 x 0.1 ml Strip Tubes 1 x Master Mix Block, 5 x 5 ml 1 x Master Mix Block, 1 x 5 ml, 4 x 2 ml 1 x Master Mix Block, 1 x 5 ml, 4 x 1.5 ml 1 x Reagent Block, 16 x 0.2 ml / 2 ml Flat / 1.5 ml Tapered Tubes 4 x Tip Rack Holder for 96-Tip Rack.
• HEPA filter: preinstalled dual-cartridge 3M Air-Mate HEPA filter system provides positive pressure clean air within the closed hood
• Preinstalled UV lamp for workable decontimation
• Operating temperature, 15–30 °C (59–86°F)

Location: FA 312 (Shared Core/Equipment room, door code access required)

The GeneSys spectrophotometer performs high-throughput quantitative UV-Vis measurements where a double beam is required as a reference cell position. Optimized for usability and performance, this system features a high-resolution color touchscreen, and optional Wi-Fi networking. The compartment is a 8-position cell changer (standard).

Key features of the GeneSys 180 UV/VIS include:

• Double Beam/Reference Cell
• Standard 8-position cell changer with switchable turret
• Room light resistance for 'open-lid' operation
• Accommodates cells up to 100 mm pathlength
• Exports data to a USB drive or directly to your computer via a USB cable

Location: FA 314 (Tissue Culture facility, door code access required)

The Qubit 4 Fluorometer accurately measures DNA, RNA, and protein quantity. The Qubit together with a RNA IQ Assay Kit can accurately distinguish intact from degraded RNA in just two easy steps. For all Qubit assays, the concentration or quality of the target molecule in the sample is reported by a fluorescent dye that emits a signal only when bound to the target, which minimizes the effects of contaminants on the result. The easy-to-use touch-screen menus make it easy to select and run the assays you need, with results displayed in just a few seconds.

Key features of the Qubit 4 Fluorometer include:

• Quantitation of DNA, RNA, and protein in less than three seconds per sample
• Measures intact RNA in less than 5 seconds per sample
• High levels of accuracy using only 1–20 μL of sample, even with very dilute samples.
• Stores results from up to 1000 samples
• Large 5.7-inch, state-of-the-art color touch screen for easy workflow navigation
• Graphical display indicates when samples are in the extended range or out of range
• Exports data to a USB drive or directly to your computer via a USB cable