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What types of instruments are available at AMCF?

AMCF offers a range of state-of-the-art microscopes and cytometers. In addition, the facility is home to a number of benchtop instruments (e.g., microplate readers, gel and membrane imagers, etc.) and a large range of sample preparation equipment. For data analysis, several software packages are available in the computer lab MH2 L.09.337.

For a complete listing of bookable instruments, log in to PPMS and click Schedules on the top menu.

More information about individual instruments is available here: 

For some instruments, there are basic instruction videos available (links in the tables below).

Light microscopy

Advanced light microscopy systems.

Type Systems available Applications Keywords User instructions, links, etc.
Confocal point-scanning LSM780, LSM800, LSM880, STEDYCON High-end fluorescence; 3D imaging; time-lapse (minutes and hours) Inverted stands; stage-top incubation; lambda scan; linear unmixing; FRET; FRAP LSM780 training video LSM800 training video
Widefield Axio Observer 7, Axio Imager Fluorescence, brightfield, darkfield Inverted and upright stands  
Live-cell Celldiscoverer 7, BioStation IM-Q Timelapse (hours and days); fluorescence and brightfield Inverted; multiple plate formats supported; liquid handling supported  
Automated/high-throughput/high-content Celldiscoverer 7, VS120 Automated slide scanning; screening assays; fluorescence and brightfield Virtual microscopy; quantitative microscopy  
Documentation Primo Vert, Axio Scope Documentation; demonstrations; teaching Main lab; cell lab; wifi camera  
Stereo/zoom Stemi 305, Axio Zoom V.16 Developmental biology; fluorescence and brightfield  Model organisms; large specimens  
Super-resolution LSM800, LSM880, Elyra PS.1, STEDYCON Super-resolution imaging Airyscan, SIM, SMLM, STED  

Confocal spinning-disk

Yokogawa CSU-X1 Fast 3D imaging/timelapse (minutes and hours) Inverted; Petri dish format  
Fast widefield Sutter DG-4/Qimaging EM-CCD Ratio imaging (e.g., Fura-2)    

Electron microscopy

Transmission and scanning electron microscopes.

Type Systems available Applications (detectors) Keywords
Transmission HT7800 TEM, STEM (brightfield and darkfield), TEM tomography 3 specimen holder; Rotation holder +/- 60 degrees
Scanning  Sigma HV SEM (Inlens , SE , Backscattered ) 9 stubs sample holder
Scanning GeminiSEM 300Atumtome SEM (Inlens, SE, VPSE, ESB, array tomography) 9 stubs sample holder
Scanning Merlin VP Compact SEM (Inlens, SE,  EDS, EBSD, WDS, CL, VP, AsB, CC) 9 stubs sample holder, 70 degrees fixed sample holder

Flow cytometry

Flow cytometers and cell sorter.

Type Systems available Applications Keywords
Flow Fortessa,
Accuri C6 plus
Classical flow cytometry (violet, blue, yellow/green, red) Single tubes and high throughput sampler
Flow + sort Aria III Classical flow cytometry + sorting (violet, blue, yellow/green, red) 4-way sorting in tubes, ACDU for sorting in microplates
Imaging flow ImageStream Imaging flow cytometry (violet, blue, yellow/green, red)  
Spectral flow   Spectral flow cytometry (violet, blue, red)  
Hematology analyzer ProCyte Dx CBC analyses  

Other instruments

Benchtop instruments and sample preparation equipment.

Type Systems available Applications Keywords User instructions, links, etc.
Scanner Odyssey CLx, Typhoon 5 RGB fluorescence, IR fluorescence, densitometry, phophor imaging Gels and membranes  
Imager LAS 3000, LAS 4000 Chemiluminescence, RGB fluorescence, Trans-UV Gels and membranes  
Microplate reader ClarioSTAR, Synergy H1 UV-VIS absorbance, fluorescence, luminescence, fluorescence polarization Incubation available (BioSpa 8) Synergy H1 training video
Sample prep BioWave, EM ICE, AFS2, EM Trim, EM KMR3 Microwave processing, high pressure freezing, freeze substitution, block trimming, glass knifemaker    


UC6, UC7, PowerTome PC, Ultracut E Ultrathin sectioning, ultrathin cryosectioning (Tokuyasu technique), ATUM    
Cryostat CryoStar NX70 Cryosectioning    
Vibratome VT1200S Fresh and fixed tissue sectioning   Keycard
NTA ZetaView Nanoparticle tracking analysis Scatter and fluorescence (excitation 488 nm)  


Image analysis software packages available at the data analysis lab (L09.337) at AMCF.

FlowJo licenses (1 month access) can be ordered through PPMS and you can then run the program on your own PC after logging in to Flowjo Portal. Additionally, there is one license available for booking through PPMS.

Type Software Applications Keywords
Open-source Fiji/ImageJ2 All-purpose image analysis Available on all analysis PCs


Quantification, restoration, visualization Available on analysis PCs 25 and 26
NB! This software has been discontinued by PerkinElmer and is no longer updated.
Commercial Imaris Quantification, restoration, visualization Avaliable on analysis PC 27
Commercial Vision 4D 3D visualization for serial SEM Available on analysis PC 27
Commercial Radius Image analysis for TEM  Available on analysis PC 28
Open-source CellProfiler High-content image analysis Available on analysis PC 25 and 26
Open-source QuPath Large-area image analysis (virtual slide formats, also brightfield) Available on analysis PC 27
Commercial ZEN Blue Image analysis, deconvolution, batch processing 

Available on analysis PC 25, 26, and 29
ZEN Lite free download

Commercial Huygens Essential Deconvolution Available on analysis PC 29
Commercial FlowJo Flow cytometry data analysis Access through FlowJo portal (order license first in PPMS)
Commercial GraphPad Prism Statistical analysis and graphing Available on analysis PC 27

Links to training resources

There are excellent training videos and other types of material available online. Below are some links to useful resources on instruments and techniques, data analysis, and figure preparation.

  • YouTube playlist on scientific figure preparation using Adobe Illustrator (from Stowers Institute for Medical Research).
  • iBiology Microscopy Course on YouTube, covering fundamentals and practicals aspects of various types of microscopy.
  • YouTube playlist demonstrating use of the QuickFigures plugin in Fiji, which is excellent for quickly producing high-quality figures from microscopy data and western blots.
  • The Center for Open Bioimage Analysis YouTube channel, with training material for several open source software packages.
  • The OiVM YouTube channel (Baylor College of Medicine), which has excellent videos explaining the principles of confocal microscopy and airyscanning, among other things.
  • Spectral unmixing in fluorescence microscopy explained by embedded ZEISS specialist Chris Hellriegel (Harvard Center for Biological Imaging).
  • Very useful Fiji training videos by Johanna M. Dela Cruz (Cornell Institute of Biotechnology).
  • Applied bioimage analysis lecture series on YouTube by Robert Haase (Myers lab, MPI CBG).