Instrument Details - Microscopy

The UCSC Life Sciences Microscopy Center manages several widefield and confocal microscopes available for use by the UCSC research community. Some are owned by the CIRM-funded UCSC Institute for the Biology of Stem Cells, and others belong to individual laboratories but are administered by the center.

The following scopes are available (click for details):

Zeiss SteREO Discovery V20 Teaching Dissection Scope

Best suited for direct observation of specimens that require a large amount (up to 110mm) of working distance and for teaching applications where simultaneous observation of specimen or procedure by student and teacher is beneficial.

Features

Stand: dual observation head with MARC remote control

Stage: motorized with focus and height control.

Transmitted light modes: direct and oblique illumination with directional or diffuse reflectors

Reflected light illumination: two variable mount LED

Magnification range: 4.7x - 94.5x

Ownership: common

Location: 319 Sinsheimer Labs

Zeiss Axiozoom Microscope

Best suited for samples normally viewed under a dissections scope and requiring large working distances, but where higher magnification is needed. Well suited for thin (less than 15 microns) samples mounted on a standard microscope slide with a coverslip. Non-labeled and fluorescently-labeled samples may be used.

Features

Stand: Axiozoom V.16

Stage: motorized stage with transmitted light

Fluorescent filters available:

DAPI: Fset49, EX 365 : DC 396 : EM BP 445/50

GFP: Fset38, EX BP 470/40 : DC 495 : EM BP 525/50

Cy3: Fset43, EX BP 550/25 : DC 570 : EM BP 605/70

Cy5: Fset50, EX BP 640/30 : DC 660 : EM BP 690/50

Transmitted light modes: bright-field, bright-field plus, relief contrast, dark-field

Objectives: 0.5x/0.125 N.A., 1x/.025 N.A., 2.3x/0.57 N.A.

Software: Zeiss Zen with Z-stack, tiling and stitching modules

Camera: Zeiss AxioCam HRm (monochrome)

Ownership: lab-owned

Location: 312 Sinsheimer Labs

Leica DM5500 B Widefield Microscope

Best suited for thin (less than 10 microns) samples mounted on a standard microscope slide with a coverslip. Non-labeled, fluorescently-labeled, and colorimetric-dye-labeled samples may be used.

Features

Stand: upright, Leica DM5500B

Stage: motorized stage for 3D stack, tiling, and multi-point image acquisition.

Fluorescent filters available:

DAPI: 116000232 EX BP 360/40 : DC 400 : EM BP 470/40

GFP: 11532366 EX BP 470/40 : DC 500 : EM BP 525/50

Texas Red: 11513885 EX 560/40 : DC 595 : EM BP 570/75

Cy5: 11600230 EX BP 620/60 : DC 660 : EM BP 625/75

Cy3: 11600231 EX 545/40 : DC 565 :

EM 610/75 (note: Cy3 cube is not normally on the scope but may be exchanged in upon request)

Transmitted light modes: bright-field, DIC, and polarized light

Objectives: 4x/0.1, 10x/0.3, 20x/0.5 (DIC), 40x/0.75 (DIC), 63x/ 0.6-1.4 oil (DIC), and 100x/1.3 oil (DIC)

Software: Leica Application Suite Advanced Fluorescence V2.6.9.7266

Camera(s): Leica DCF360 monochrome, Leica DFC450 color

Ownership: common

Location: 111 Sinsheimer Labs

Keyence Biorevo BZ-9000 Digital Widefield Microscope

Best suited for thin (less than 10 microns) samples mounted on a standard microscope slide with a coverslip, but can also accommodate samples in a small petri dish. Non-labeled, fluorescently-labeled, and colorimetric-dye-labeled samples may be used. Especially good for applications requiring image tiling or for samples that have large fluctuations along the Z-axis.

Features

Stand: inverted, Keyence BZ-9000 stand-alone unit

Stage: motorized stage for 3D stack, tiling, and multipoint image acquisition; digital navigation for eyepiece-free use

Fluorescent filters available:

DAPI: EX BP 360/40 : DC 400 : EM BP 460/50

GFP: EX BP 470/40 : DC 495 : EM BP 535/50

TRITC: EX BP 515/25 : DC 565 : EM BP 605/55

Texas Red: EX BP 560/20 : DC 595 : 630/60

Cy5: EX BP 620/60 : DC 660 : 700/75

Transmitted light modes: Bright-field and phase contrast

Objectives: 4x/0.2, 10x/0.45, 20x/0.75, 20x/0.45 ELWD Ph, 40x/0.95, and 60x/1.4 oil.

Software: Keyence View and Keyence Analyzer with dynamic cell count and measurement modules

Ownership: common

Location: 355 Biomedical Sciences

Zeiss Live-Cell Imaging Widefield Microscope

Best suited for thin (less than 10 microns) samples mounted on a standard microscope slide with a coverslip, in a culture dish, or on a multi-well plate. Non-labeled and fluorescently-labeled samples may be used. Time course experiments requiring a temperature- or CO2-controlled environment or both.

Features

Stand: inverted, Axiovert 200M

Stage: motorized stage for 3D stack and multi-point image acquisition; sample holder must be swapped to accept slides, petri-dishes, or multi-well plates.

Fluorescent filters available:

DAPI: EX 365 : DC 395 : EM BP 445/50

GFP: EX BP 470/40 : DC 495 : EM BP 525/50

TRITC: EX BP 540/25 : DC 565 : EM BP 605/55

Texas Red: EX BP 557.5/55 : DC 600 : EM LP 615

Transmitted light modes: bright-field, DIC, and phase contrast

Objectives: 2.5x/0.075, 10x/0.25 (PH1), 20x/0.3 (PH1), 40x/0.6 (PH2) (DIC), and 63x/1.4 oil (DIC)

Software: Zeiss ZEN, Pecon Incubation Remote

Camera: Zeiss AxioCam MRm (monochrome)

Ownership: lab-owned

Location: 461 Biomedical Sciences

Please note that you must have documented BSLII clearance before you can use this scope.

Zeiss AxioImager Z2 Widefield Microscope

Best suited for samples up to ~40um (with Apotome) mounted on a standard microscope slide with a coverslip. Excels when extra-contrast is needed. Non-labeled, fluorescently-labeled and colorimetric-dye-labeled samples may be used.

Features

Stand: upright, AxioImager Z2

Stage: motorized 8-slide stage for 3D stack and multi-point image acquisition;

Fluorescent filters available:

DAPI: Fset49, EX 365 : DC 396 : EM BP 445/50

CFP: Fset47, EX BP 436/25 : DC 455 : EM BP 480/40

GFP: Fset38, EX BP 470/40 : DC 495 : EM BP 525/50

YFP: Fset46, EX BP 500/25 : DC 515 : EM BP 535/30

Cy3: Fset43, EX BP 550/25 : DC 570 : EM BP 605/70

RFP: Fset63, EX BP 572/25: DC 590 : EM BP 629/62

Cy5: Fset50, EX BP 640/30 : DC 660 : EM BP 690/50

Transmitted light modes: bright-field

Objectives: 2.5x/0.12, 10x/0.45, 20x/0.8 , 40x/0.95, 40x/1.4 oil and 63x/1.4 oil Zeiss-Apo-Tome2

Software: Zeiss ZEN

Camera: Zeiss AxioCam 506 (monochrome) Zeiss AxioCam 506 (color)

Ownership: common

Location: 264 Biomedical Sciences

Please note that you must have documented BSLII clearance before you can use this scope.

Solamere Spinning Disk Confocal Microscope

Best suited for imaging of thick (10-150 microns) live samples mounted on a standard microscope slide with a coverslip, in a small dish, or in an incubation chamber. Non-labeled and fluorescently-labeled samples may be used.

Features

Stand: inverted, Nikon TE2000

Stage: motorized stage for 3D stack and multipoint image acquisition; sample holder available to accept slides, petri-dishes, and multi-well plates

Fluorescent filters available:

—for direct observation through eyepieces:

DAPI: EX BP 360/40 : DC 400 : EM BP 460/50

GFP: EX BP 470/40 : DC 495 : EM BP 525/50

TRITC: EX BP 540.5/25 : DC 565 : EM BP 620/60

—for confocal operation:

DAPI: EM 460/50

GFP+RFP: EM BP 528/80

GFP: EM BP 525/50

RFP: EM BP 593/40

Cy5: EM BP 700/75

Transmitted light modes: bright-field and DIC

Laser lines: solid state 405, 488, 561, 640

Objectives: 10x/0.3, 20x/0.50 (DIC), 40x/ 0.75, 40x/1.3 oil, 60x/1.4 oil (DIC), and 100x/1.4 oil (DIC)

Software: Micro-Manager

Scanner: Yokogawa CSUX-1 spinning disk

Camera: Hamamatsu ImageEM X2

Ownership: lab-owned

Location: 339 Sinsheimer Labs

Leica SP5 Confocal Microscope

Best suited for thick (10-150 microns) samples mounted on a standard microscope slide with a coverslip or in a small petri dish. Used for FRAP, photo-activation, and scanning irregular regions of interest. Non-labeled and fluorescently-labeled samples may be used. Can capture highly dynamic processes if operated in resonance scanning mode.

Features

Stand: inverted, Leica DMI6000

Stage: motorized stage for 3D stack, tiling, and multipoint image acquisition; sample holder will accommodate slides and small (60 mm) petri dishes

Fluorescent filters available: for direct observation through eyepieces GFP, Texas Red, and simultaneous GFP + Texas Red; filters for confocal operation are spectral (ATOF)

Transmitted light modes: bright-field, DIC, and polarized light.

Laser lines: 405, Argon (458, 476, 488, 496, and 514) and HeNe (543, 594, and 633)

Objectives: 10x/0.3, 20x/0.75, 40x/1.25-0.75 oil DIC , 63x/1.4-0.6 oil DIC, and 63x/1.2 water

Software: Leica Application Suite Advanced Fluorescence

Detectors: 3 channels available for simultaneous fluorescent image acquisition, 1 available for transmitted light image acquisition; standard scanning and fast resonance scanning (8000 Hz) modes available.

Ownership: common

Location: 111 Sinsheimer Labs

Zeiss 880 Confocal Microscope with Airyscan Fast

IMPORTANT: If you publish data generated on this scope you must cite NIH s10 Grant 1S10OD23528-01.

Best suited for thick (10-150 microns) samples mounted on a standard microscope slide with a coverslip or in a petri-dish or multi-well plate. Non-labeled and fluorescently-labeled samples may be used. Time-course experiments on thick specimens requiring a temperature or CO2-controlled environment or both.

Features

Stand: inverted, AxioObserver.Z1

Stage: motorized stage for 3D stack and multi-point image acquisition; sample holder available to accept slides, petri-dishes, and multi-well plates

Fluorescent filters available:

—for direct observation through eyepieces: DAPI, GFP, Rhodamine and mCherry

—for confocal operation:

We have the "2+1" configuration which has 1 super-cooled multi-alkali, 1 standard multi-alkali and 1 GaAsP detector. These detectors are all spectral. The Airy detector can also be used in combination with these detectors to add a 4th channel that is filter based.

—for Airyscan operation:

BP 420-480 + BP 495-550

BP 495-550 + LP570

BP 570-620 +LP645

BP 465-505 +LP 525

BP420-480+LP 605

Transmitted light modes: bright-field

Laser lines: 405, Argon (458, 488, and 514) and HeNe (561, 594 and 633)

Objectives: 10x/0.45, 20x/0.80, LD 20x/0.4 corr, 40x/ 0.95 corr, 63x/1.4 oil (DIC).

Software: Zeiss ZEN Black for microscope control, ZEN Blue for additional processing

Detectors: 4 channels available for simultaneous fluorescent image acquisition, 1 channel available for transmitted light image acquisition

Ownership: common, but access must be approved by 880 confocal oversight committee until further notice. Detail about our access policy for this scope can be found here.

Location: 264 Biomedical Sciences

Please note that you must have documented BSLII clearance before you can use this scope.

Olympus Multi-Photon Microscope

Best suited for very thick (30-1200 microns) samples mounted on a standard microscope slide or in a petri dish and for imaging large live specimens. The antibody penetration depth may limit imaging of fixed and stained samples thicker than 30 microns. Genetically encoded fluorophores are recommend for deep imaging. Samples thicker than 240 microns may require clearing.

Note: Laser safety training is mandatory for all users.

Features

Stand: upright, Olympus BX61WI

Stage: Prior Z-deck motorized stage for 3D stack, tiling, and multi-point image acquisition; sample holder will accommodate slides, petri dishes and live animals.

Fluorescent filters available: for direct observation through eyepieces GFP, Texas Red, and DAPI.

Transmitted light modes: bright-field, when condenser is in place and for direct observation through eyepieces only.

Laser: SpectraPhysics MaiTai DeepSee HP with tunable excitation from 690-1040nm.

Objectives: 10x/0.3, 25x/1.05N.A. water immersion

Software: Olympus FV1000 ASW

Detectors: 3 channels available for simultaneous fluorescent image acquisition, there are 4 NDDs total.

Ownership: common

Location: 109c Sinsheimer Labs

JEOL 1230 Transmission Electron Microscope (TEM)

Best suited for ultrastructure examinations of specimens prepared by negative staining, metal shadowing, immune-EM or by ultrathin sectioning, tomography, and cryo-EM.

Features

Voltage: 120 keV

Stage: computer-controlled

Low-dose kit

Software: Gatan DigitalMicrograph

Camera: Gatan 4k by 4k CCD

Ownership: lab-owned

Location: C230 Earth and Marine Sciences

Image Analysis Workstation

Best suited for post-acquisition processing and analysis of images where image processing software is operating-system-specific and where operations are RAM-intensive. Helps keep microscopes and image acquisition computers available for data acquisition.

Software:

—FIJI - Image J

—Zeiss LSM Browser

—Leica AF Lite Viewer

—Microsoft Excel

—Keyence Analyzer with Dynamic Cell Count and Measurement modules

—Keyence resizer

Ownership: common

Location: 111 Sinsheimer Labs

BioMed Image Analysis Workstation

Best suited for post-acquisition processing and analysis of images where image processing software is operating-system-specific and where operations are RAM-intensive. Helps keep microscopes and image acquisition computers available for data acquisition.

Software:

—Imaris

—AutoQuantX3

—Neurolucida

—Zeiss ZEN

—FIJI - Image J

—Zeiss LSM Browser

—Zeiss ZEN Lite

—Leica AF Lite Viewer

—Microsoft Office

—Keyence Analyzer with Dynamic Cell Count and Measurement modules

—Keyence resizer

Ownership: common

Location: 264 BioMed