Equipment – Microscopes & Workstations

The links below lead to brief descriptions of each instrument (along with videos), but a very detailed table with specifications and usage fees can be found here:

Spreadsheet table view of all MIC equipment

The rate for External Users is 2x the published UC rate. We also have offline computer workstations for image processing. Instrument scheduling can be found on the MIC iLabs page. Please contact us with any questions or specific imaging needs.

Our equipment falls into five general categories:



TrinityZeiss LSM 880 NLO AxioExaminer with Airyscan and Coherent Chameleon Vision (Trinity)

– Ultra-sensitive, upright laser scanning confocal with 1-photon and 2-photon imaging, GaAsP detectors, 34-channel spectral imaging
– Airyscan super-resolution technology, up to 1.7-fold better resolution than standard scanning confocal microscopes
– Large motorized stage for combined electrophysiology and imaging
– 20X CLARITY objective in addition to standard objectives

NeoZeiss LSM 880 NLO AxioExaminer with Coherent Chameleon MPX OPO (Neo)

– Ultra-sensitive, upright confocal imaging with large motorized fixed stage
– 2-photon imaging from 700-1300 nm
– Visible lasers: 405, 458, 488, 514, 561, 591, 633nm

Rachel copyZeiss LSM 780 AxioExaminer with Spectra-Physics Maitai (Rachel)

– Ultra-sensitive, upright confocal featuring 2-photon imaging with GaAsP detectors
– 34-channel spectral system with imaging in the visible range from 400-700nm; visible lasers: 405, 488, 514, 561, 633nm
– Large fixed stage for combined electrophysiology and imaging

Optimus copyZeiss LSM 710 AxioObserver (Optimus Prime)

– Inverted laser scanning confocal with 34-channel spectral detection
– Motorized XY-stage for tile scan and multi-position experiments
– Live cell imaging capabilities: full incubation chamber with temperature, CO2 control and heated stage
– Lasers: 405, 458, 488, 514, 561, 591, 633nm

MF3i/Sutter In Vivo 2p Movable Objective Microscope with 2p Phasor SLM(Millenium Falcon)

– Dual-multiphoton Movable Objective Microscope (MOM) system uniquely designed for in vivo optogenetic studies using a Spatial Light Modulator (SLM) for stimulation at 1040nm with high-power femtoTrain laser
Special training required. 

Pris copyZeiss LSM 510 META NLO AxioImager with Maitai DeePSee (Pris)

– Upright confocal and multiphoton laser scanning microscope with a Spectra-Physics MaiTai HP DeepSee laser for 2-photon Imaging (700nm – 1020nm)



Nikon Spinning Disk Confocal (Wall-E)

– Inverted Yokogawa spinning disk confocal microscope for live cell imaging
– Nikon PerfectFocus
– Lasers: 405, 488, 561, and 637nm
– Full incubation enclosure with CO2, humidity, and heating
– Motorized XY stage

Enterprise copy3i Spinning Disc Confocal with SLM (Enterprise)

– Upright spinning disk confocal microscope with spatial light modulator (SLM)
– Large platform, Sutter-motorized XY-stage for electrophysiology
– Ideal for zebrafish, Drosophila, and brain slice work with 1-photon or 2-photon holographic stimulation

Max copyNikon/Andor Spinning Disk Confocal (Max)

– Inverted spinning disk confocal with a motorized XY-stage and Nikon PerfectFocus
– Full enclosure incubation chamber for humidity, CO2 and temperature control for live cell imaging.
– Andor Clara and Andor iXon cameras



Morpheus copy
Zeiss LightSheet.Z1 CLEARING (Morpheus)

– Selective Plane Illumination Microscopy (SPIM)
– Setup for cleared tissue imaging – CLARITY, CUBIC


Zeiss LightSheet.Z1 (Serenity)

– Selective Plane Illumination Microscopy (SPIM)
– Water-based samples only – e.g., zebrafish, tadpoles, Drosophila



BayMax copy

Zeiss Axio Scan.Z1 Slide Scanner(Baymax)

– 100-slide automated slide scanner for fluorescence or IHC
– Filter cubes for: DAPI, eGFP, Cy3, mPlum, Cy5
– Slide scanning service available

Echo Revolve (Bender)

Bright-field and fluorescence microscope with 10x and 20x objectives which can rotate to be inverted or upright. Super easy to use, runs on an iPad, and can be used for checking your fluorescence signals prior to confocal or slide scanning!


Herzmark copyNikon Widefield Epifluorescent Microscope (The Herzmark)

– Inverted compound microscope with DIC optics
– Incubation chamber, motorized stage, and Nikon PerfectFocus
– Filters: DAPI, eGFP, Rhodamine, Cy5 (?)

Zoom copyZeiss AxioZoom v16 FL (Zoom)

– Macro scope with 16x motorized zoom, fluorescence, BF transmitted or reflected light
– Motorized XY-stage, ideal for multi-position or tiling
– Fluorescent illumination with the following filter cubes: DAPI, eCFP, eGFP, eYFP,  and mCherry

Johnny5 copyLeica M205 Fluorescent Stereoscope (Johnny-5)

– Fluorescent stereoscope ideal for screening and dissections
– Filter cubes: CFP, GFP, YFP, and DS-Red
Not equipped with a camera – for screening only.




– Windows workstation with GPU processor and SSD hard drives for faster processing and rendering
– Software: Bitplane Imaris, Zeiss Zen, FIJI, Matlab, Adobe Suite

Morpheus Processing Workstation(s)

– Windows workstation with GPU processor for faster processing and rendering
– Software: arivis Vision4D, Zeiss Zen, FIJI


Serenity Processing Workstation

– Windows workstation processing lightsheet data
– Software: Zeiss Zen, FIJI



– MacPro for offline analysis
– Matlab, FIJI, Adobe Suite, Microsoft Office