Advanced Microscopy Core Facility
Instruments
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 | Ratiometric imaging (e.g., Fura-2, or mKeima) or GFP-RFP combinations | Inverted; Petri dish format |
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 300, Atumtome | 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 | ID7000 | 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 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 | ||
| Sample prep | TP1020 | Automatic tissue processor | Fixation, dehydration and infiltration of histological tissue samples | |
| Sample prep | EG1150H | Embedding station | Paraffin embedding of histological tissue samples | |
| Sample prep | Cytospin 4 | Cytocentrifuge | Produce monolayers of cells onto glass slides from any fluid suspension | |
| Sample prep | HybEZ-II | Programmable slide incubator with batch slide processing system | Conduct hybridization and incubation steps under controlled temperature and humidity conditions | |
| Rotary microtome | HS355S | FFPE tissue sectioning | Fully automated; equipped with Cool-Cut and STS | |
|
Ultramicrotome |
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) |
Software
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 |
| Commercial | 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 |
| 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).
- Excellent CellProfiler tutorials (with training material).
