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 (wd) 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 NA (wd - 114mm)
1x/.025 NA (wd- 56mm)
2.3x/0.57 NA (wd-10.6mm)
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 NA (wd-18mm)
10x/0.3 NA (wd-11mm)
20x/0.5 NA (DIC) (wd-1.15mm)
40x/0.75 NA (DIC) (wd- 0.40mm)
63x/ 0.6-1.4 NA oil (DIC) (wd-0.1mm)
100x/0.7-1.4 NA oil (DIC) (wd-0.09mm)
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 NA (wd-20mm)
10x/0.45 NA (wd-4mm)
20x/0.75 NA (wd-1mm)
20x/0.45 NA ELWD Ph (wd- 6.9-8.2mm)
40x/0.95 NA (wd-0.25-0.17mm)
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 NA (wd -8.7mm)
10x/0.25 NA (PH1) (wd-4.5mm)
20x/0.3 NA (PH1) (wd-4.3mm)
40x/0.6 NA (PH2) (DIC) (wd-0.75mm)
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 NA (wd-8.7mm)
10x/0.45 NA (wd-2mm)
20x/0.8 NA (wd-0.55mm)
40x/0.95 NA (wd-0.25mm)
40x/1.4 NA oil (wd-0.21mm)
63x/1.4 NA oil (wd-0.19mm)
Special Feature: Zeiss-Apotome 2
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 NA (wd-16mm)
20x/0.50 NA (DIC) (wd-not available)
40x/0.75 NA (wd-0.66mm)
40x/1.3 NA oil (wd-0.2mm)
60x/1.4 NA oil (DIC) (wd-0.13mm)
100x/1.4 NA oil (DIC) (wd-not available)
Software: Micro-Manager
Scanner: Yokogawa CSU-X1 spinning disk
Camera: Hamamatsu ImagEM X2
Ownership: common
Location: 111 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 NA (wd-11mm)
20x/0.75 NA (wd-0.59mm)
40x/1.25-0.75 NA oil DIC (wd-0.1mm)
63x/1.4-0.6 NA oil DIC (wd-0.1mm)
63x/1.2 NA water (wd-0.14mm)
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 NA (wd-2.0mm)
20x/0.4 NA, corr LD (wd-8.4mm)
20x/0.8 NA (wd-0.55mm)
40x/0.95 NA corr (wd-0.25mm)
63x/1.4 NA oil (wd-0.19)
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.
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