Advanced Light Microscopy

Storrs

Center for Open Research Resources and Equipment

The Advanced Light Microscopy Facility provides access to advanced imaging technology in order to promote innovation and cross-disciplinary interaction. The facility houses a number of laser scanning confocals, as well as systems for widefield imaging and total internal reflection microscopy.

Facility Homepage

Microscope reservations can be made no more than 14 days in advance.
Reservations can be made in 15 min increments starting on the quarter hour.
There is no maximum reservation time limit.
Changes or cancellations to reservations can be made up to 6 hours in advance. After that, the full cost of the reservation will be charged.
The actual reservation time plus any additional time used will be billed automatically.
Reservations will be automatically cancelled if not started within 30 min.
Once per user, per calendar month, a billing adjustment can be made for a cancelled/changed reservation. Requests must be made to Chris O’Connell by email

Service Requests

Assisted sessions and instrument training can be requested by filling out the Service Request Form. Rates for instruments and service can be found here. After your form is received, you will be contacted to arrange a brief meeting to discuss your projects imaging needs to determine whether assisted sessions or training are necessary, the best instrument for your application, and any sample preparation considerations. Refer to the below flowchart which outlines the process for using the facility.

Service Request

Leica SP8 Spectral Confocal

This is an inverted confocal microscope with five filter-free spectral and individually regulatable channels including four standard PMT detectors and one high-sensitivity HyD detector with photon counting capacity. The scanner also includes both standard galvo scan mirrors and an optional 8 KHz resonant scanner for high speed imaging. Use of an acusto-optical beamsplitter (AOBS) instead of traditional dichroic mirrors makes this microscope also suitable for reflected light microscopy applications. The instrument is housed in the Bioscience Electron Microscopy Laboratory located in the Biology and Physics Building (BPB), room G10.

Location:

Bioscience Electron Microscopy Laboratory

Biology and Physics Building (BPB), room G10.

Specifications:

Microscope:

Inverted Stand DMI 6000
Motorized stage
Super Z Galvo stage

Lasers:

405 nm Diode laser
Argon/2 (458, 488, 514 nm)
561 nm DPSS laser
633 nm HeNe laser

Scanners:

Continuously adjustable non-resonant scanner (1-1800 Hz)
Resonant scanner (8000 Hz) – 28 fps at 512 x 512

Objective Lenses:

10x/0.30 HC PL FLUOTAR
20x/0.75 HC PL APO IMM CORR CS2
40x/1.30 HC PL APO OIL CS2
63x/1.40 HC PL APO OIL CS2
100x/1.40 HCX PL APO OIL CS

Detectors:

Four PMTs
One HyD
All filter-free spectral and individually regulatable detectors
Transmitted light brightfield detector (with DIC option)

Software:

LAS X for image acquisition, processing, and quantification

Nikon AXR Confocal + TIRF

The Nikon AXR is a point scanning confocal built around the inverted Ti2E microscope. The large 25 mm field of view and resonant scanner are optimized for rapid imaging of samples. The DUX-VB confocal detector features 4 sensitive GaAsP detectors that can be flexibly configured for a range of dyes via spectral detection. 6 laser lines provides a range of excitation options for a variety of fluorescent dyes. In addition to confocal microscopy, the system has an iLAS2 illumination module for TIRF imaging. This device can perform simultaneous TIRF imaging and photostimulation. TIRF, widefield, and transmitted light images are collected on a Photometrics Prime 95B sCMOS camera. The instrument is located in the Biology and Physics Building (BPB), room G05D.

Specifications:

Microscope:

Inverted microscope Nikon Ti2E
Motorized x/y stage
PerfectFocus optical z drift correction
MCL Nano-Z200 piezo z stage

Laser Unit for Confocal:

LUA-S6 405/445/488/514/561/640

Laser Unit for TIRF:

LUNF XL 405/488/561/640

TIRF/Widefield Camera:

Photometrics Prime95B

Objective Lenses:

10X PLAN APOCHROMAT LAMBDA D, DIC
20X PLAN APOCHROMAT LAMBDA D, DIC
40X/1.30 PLAN FLUOR, Oil, DIC
60X/1.40 PLAN APOCHROMAT LAMBDA D, Oil, DIC
100X/1.45 PLAN APOCHROMAT, Oil, DIC
100X/1.49 APO TIRF, Oil, DIC

Software:

NIS-Elements C Confocal Package, JOBS for Scanning Plates and Creating Custom Acquisition and Analysis Routines, NIS-Elements 2D/3D, Deconvolution Suite, NIS.ai Artificial Intelligence Module, General Analysis 2 and 3

Location:

Bioscience Electron Microscopy Laboratory

Biology Physics Building (BPB), room G10.

Specifications:

Hardware:

HP Z640 Workstation
30″ Z30i LED-LCD Monitor
Microsoft Windows 7 Professional Edition 64bit OS
NVIDIA Quadro K2200 4GB Graphics Card
Intel® Xeon E5-1660v3 3.00GHz 20MB 2133 8C CPU
64GB RAM
2 TB striped RAID data drive

Software:

Leica LAS X including the following modules:
- 2D Analysis, 3D Analysis, and 3D Visualization
NIS-Elements AR including the following module:
- Deconvolution
Image J

Lasers:

405, 488, 561, 638 nm

Imaging Optics:

5X 0.16NA (for live samples in aqueous media)
5X 0.16 NA (for fixed samples, correction collar adjustable for different refractive index media up to RI=1.53)
10X NA 0.5 (for live samples in aqueous media)
20X NA 1.0 (for live samples in aqueous media)
20X NA 1.0 (for fixed samples, correction collar adjustable for different refractive index media up to RI=1.45)

Illumination Optics (2 each for forming the lightsheet):

5X NA 0.1
10X NA 0.2

Imaging Chambers:

Live chamber for samples in aqueous media
Fixed sample chamber (small)
Fixed sample chamber (large, 28 x 31 x 49 mm)

Detectors:

2 PCO edge 4.2 sCMOS cameras for dual channel imaging
- 2048 x 2048 pixel resolution
- 100 fps maximum frame rate
- up to 82 % quantum efficiency

Software:

Zen Black for acquisition
Zen Blue for analysis
Arivis for large volume 3D rendering and analysis (on separate analysis PC)

Abberior Instruments 3D STED

This is an inverted confocal microscope that uses stimulated emission depletion (STED) of fluorescent dyes to obtain super resolved images. There are four pulsed excitation lasers and two pulsed STED depletion lasers for imaging. The instrument is capable of 2D or 3D super resolution imaging using spatial light modulators to shape the depletion beams in the x-y and z axes. The instrument is housed within the Bioscience Electron Microscopy Laboratory located in the Biology and Physics Building (BPB), room G11.

Microscope:

Inverted Stand Olympus IX83
Motorized x-y stage
Physik Instrumente piezo z stage insert

Lasers:

Excitation

405 nm CW (non-STED imaging)
440 nm pulsed
485 nm pulsed
561 nm pulsed
640 nm pulsed

STED Depletion

595 nm pulsed
775 nm pulsed

Scanner:

Continuously adjustable QUADScan galvo scanner (up to 2600 Hz line scanning)

Objective Lenses:

10X/0.3 UPLFLN10X2
20x/0.75 UPLSAPO20
40x/0.1.3 UPLFNL40 oil immersion
60x/1.2 UPLSAPO60 water immersion
100x/1.40 UPLANSAPO oil immersion

Detectors:

Four filter-based APD detectors

Software:

Abberior Impsector for acquisition and visualization

Leica Thunder Imager

The Leica Thunder Imager is an upright microscope for fluorescence, transmitted light, and true color imaging . With a stage capable of holding up to 8 slides, this instrument is optimized for high throughput imaging of cells and tissue sections. Fluorescent images can be processed with Leica’s computational clearing and deconvolution to remove out of focus blur, enhance contrast, and sharpen details. The software Navigator function can be used for rapidly generating sample overviews for subsequent selection of areas of interest. The instrument is located in the Biology and Physics Building (BPB), room G05D.

Services and Rates

The Advanced Light Microscopy Facility provides training and access to advanced light microscopy systems at an hourly rate. In addition, we are available to consult with and support users at every stage of a project including: experimental design, sample preparation, image acquisition, analysis, and data preparation.

Consultation: We are available to meet with current and potential users to advise on sample preparation and the selection of the instrument that best serves the research requirements.
Training: All users are provided with training that covers facility policies and details of instrument operation.
Instrument Access: Researchers are able to independently use the instruments after training, or they can work with the Director in assisted sessions. See Instrumentation for current rates.
Support: Our expertise is always available to help maximize the impact of the instruments on users’ studies through further consultations or by scheduling assisted sessions with the Director on the microscope.
Education: The Facility gives workshops and lectures on microscopy applications and image analysis to advance the microscopy knowledge of the research community.
Billing: Monthly usage is tabulated and billing is executed by the Center for Open Research Resources and Equipment (COR2E).

Microscopy Resources

Fluorescence Spectra Viewers
ThermoFisher SpectraViewer
FPbase

Microscopy Software
Fiji (ImageJ bundled with useful plugins)
Bioformats Plugin
ImageJ Forum

Center for Open Research Resources and Equipment