Confocal Microscopy

Colorful illustration of a neuron with branching dendrites on a black background.
Mature rat cortical neuron stained for pre- and postsynaptic puncta (VGLUT1 and PSD95), imaged using a Nikon HTS spinning-disc confocal/widefield microscope. (Yara Khatib / UC Davis)
Confocal microscope with binocular eyepieces and transparent environmental chamber on a vibration-isolated table.
A front view of the Zeiss LSM 980 confocal microscope with binocular eyepieces and an environmental chamber for live-cell imaging.
Microscope objective positioned above a glass slide illuminated with blue light on a motorized stage.
Close-up of the Zeiss LSM 980 microscope stage with an illuminated sample positioned beneath the objective lens.
Red and white neurite-like structures radiate from a central point against a black background.
Immature rat cortical neuron stained for F-actin, imaged using a Nikon HTS spinning-disc confocal/widefield microscope with 405 nm photostimulation, enabling high-speed imaging up to 100 Hz (confocal) and 1000 Hz (widefield). (Yara Khatib / UC Davis)
Close-up of a transparent microscope incubation chamber with tubing and a printed connection diagram.
Detail of the Zeiss LSM 980 environmental incubation chamber, which maintains stable conditions during long-term imaging.
Touchscreen control panel displaying microscope settings, mounted beside laboratory imaging equipment.
The Zeiss LSM 980 control interface, used to adjust objectives, illumination, and imaging parameters during experiments.
Microscopic view showing cells with purple and green fluorescence highlighting structures.
Low-methylesterified pectin (green) accumulates at tricellular junctions (white arrows) in olive fruit abscission zone cells. Imaged using a Zeiss LSM 980 confocal microscope. (MinMin Wang / UC Davis)
Close-up of a Nikon HTS microscope objective positioned above an illuminated glass slide on the stage.
Close-up of the Nikon HTS microscope stage with a glass slide illuminated beneath the objective lens.
Nikon HTS microscope with binocular eyepieces and mounted imaging components in a laboratory setting.
The Nikon HTS microscope system, shown with motorized components and integrated imaging hardware.
A glowing purple shape with scattered white dots against a black background.
Hydra vulgaris (cnidarian polyp) following bisection and fixation, showing p-ERK (magenta), a marker of injury response and proliferation, in nuclei throughout the body column and wound site. Hoechst stain (white). Imaged using a Zeiss LSM 980 confocal microscope. (Iris Juanico / UC Davis)
Overhead view of a Nikon HTS microscope stage with a sample illuminated by blue light beneath the objective.
Top-down view of the Nikon HTS microscope stage during imaging, with blue light illuminating the sample.
Microscopic view of a blue and orange abstract structure with varying textures.
Fluorescently labeled Entamoeba histolytica (turquoise) performing trogocytosis (“cell nibbling”) of an insect host cell (orange). The image captures scission of the internalized host cell fragment. Imaged using a Zeiss LSM 980 confocal microscope. (Wesley Huang / UC Davis)
Close-up of the Nikon HTS binocular eyepieces with the microscope body visible in the background.
Detail view of the Nikon HTS binocular eyepieces, used for direct visual inspection during experiments.
CrestOptics X-Light DeepSIM V3 imaging system with microscope and computer monitor displaying microscopy data.
The CrestOptics X-Light DeepSIM V3 super-resolution imaging system integrated with a microscope and computer display for advanced fluorescence imaging.
Colorful abstract sculpture with swirls of yellow, green, pink, and blue against a black background.
Drosophila melanogaster female reproductive organs (uterus, vagina, accessory glands, and sperm storage organs), showing DAPI-stained nuclei and expression of three genes with distinct compartment-specific patterns in the uterus. Imaged using a Zeiss LSM 980 confocal microscope.
Close-up of CrestOptics X-Light DeepSIM V3 imaging hardware with camera and optical illumination components.
Close-up of the CrestOptics X-Light DeepSIM V3 hardware, showing the camera, illumination unit, and optical components.
Microscopic view of cells with purple and green highlights against a black background.
Callose (green) accumulates in olive fruit abscission zone cells. Imaged using a Zeiss LSM 980 confocal microscope. (MinMin Wang / UC Davis)
Angled view of a microscope integrated with the CrestOptics X-Light DeepSIM V3 imaging system.
Angled view of the microscope integrated with the CrestOptics X-Light DeepSIM V3 system, highlighting the eyepieces, stage, and optics.
Monitor showing a stitched fluorescence microscopy image generated by the CrestOptics X-Light DeepSIM V3 system.
Computer monitor displaying a high-resolution, stitched fluorescence image acquired using the CrestOptics X-Light DeepSIM V3 system.
3D visualization of a cell structure with blue and orange components.
Fluorescently labeled Entamoeba histolytica (turquoise) performing phagocytosis of an insect host cell (orange). Imaged using a Zeiss LSM 980 confocal microscope. (Wesley Huang / UC Davis)

Confocal microscopy provides high-resolution optical sectioning of biological specimens by rejecting out-of-focus light. This enables the creation of crisp 3D reconstructions from live or fixed samples. Traditional point-scanning confocal systems offer excellent resolution and flexibility but can cause photodamage over long time courses. To address this, spinning disk confocal systems illuminate the sample through thousands of pinholes simultaneously, dramatically reducing exposure per point and enabling gentle live-cell imaging.

In our facility, we offer both laser scanning and spinning disk confocal systems, including the Zeiss LSM 980, Nikon HTS, and CrestOptics X-Light DeepSIM/V3.

Benefits of confocal approaches:

  • High spatial resolution with optical sectioning
  • Compatible with both live and fixed samples
  • Fast acquisition with spinning disk systems
  • Straightforward sample preparation using standard fluorescent labeling
  • Zeiss LSM 980
  • A laser scanning confocal microscope that can image fixed and live specimens at high speeds. It has a light-efficient beam path with up to 36 simultaneous channels and high spectral flexibility. The LSM 980's fast multiplexed Airyscan 2 detector allows super-resolution imaging at 8x faster speed.
  • Nikon HTS
  • Spinning disc confocal microscope/ widefield microscope allowing high energy photo stimulation at 405 nm, facilitating imaging at frame rates of up to 100 Hz in confocal and 1000 Hz in widefield mode over a 25 mm field of view.
  • CrestOptics X-Light DeepSIM/V3
  • Versatile, live cell imaging suitable, combining spinning disc confocal  with structured illumination imaging covering the entire optical spectrum with 7 laser lines. It combines one of the highest acquisition speeds, with up to 1000 Hz across a 25 mm field of view in confocal mode.