How to use this
Answer each question with what your experiment actually needs, not what would be cool to have. The tree ends at one of our three super-resolution instruments, with a one-line rationale. Click through to that instrument’s equipment page and SOP.
If your sample doesn’t fit any leaf, talk to an imaging scientist. AMF now hosts three confocals (AX with NSPARC, A1R HD25, A1), so most confocal needs are covered in-house; for thick-tissue, lightsheet, or 2-photon work we can route you to other ICMS facilities.
The tree
1. Do you need to break the diffraction limit?
No, conventional resolution is fine
You only need optical sectioning, deeper into the sample
Confocal microscopy at AMF. Three options:
- Nikon AX with NSPARC — modern point-scanning confocal with NSPARC super-resolution detector (~120 nm lateral). General go-to for high-resolution confocal on cells in AdBio Lab.
- Nikon A1R HD25 — 25 mm field of view, 8 kHz resonant scanner, 6 lasers, two temperature-controlled stages. Best for fast scanning, large FOV, and temperature-jump experiments. Hosted by Janne-Mieke Meijer’s group, Flux.
- Nikon A1 — older Nikon confocal sharing the Ti2 body with the Abbelight SMLM in Flux 4.102. Good for routine confocal work and for users already on the Abbelight platform.
You want very low background, near the coverslip (e.g. membranes)
TIRF microscopy. The Abbelight SAFe-360 supports TIRF excitation and can run as a TIRF microscope when super-resolution is not required. Abbelight SAFe-360.
Yes, super-resolution
Is your sample alive during imaging?
Yes, live cells
Do you need single-molecule resolution (sub-50 nm)?
Possible on the Oxford NanoImager and Abbelight SAFe-360 — both support live-cell imaging with appropriate live-SMLM strategies (dSTORM with switchable buffers, DNA-PAINT for slower dynamics, single-particle tracking on TIRF).
Important: live cells run only in sealed sample chambers; standard biosafety rules apply (BSL classification, autoclave + waste disposal protocol, no open-dish work). Coordinate the protocol with an imaging scientist before booking. For very high temporal resolution or live-SIM, we may also point you elsewhere on campus.
Important: live cells run only in sealed sample chambers; standard biosafety rules apply (BSL classification, autoclave + waste disposal protocol, no open-dish work). Coordinate the protocol with an imaging scientist before booking. For very high temporal resolution or live-SIM, we may also point you elsewhere on campus.
Sub-cellular dynamics, around 50 to 100 nm
Abberior STED ExpertLine. Confocal/STED hybrid. Live STED is feasible with the right fluorophores (paint with care).
SOP coming soon.
SOP coming soon.
No, fixed cells
Many fluorophore channels, high throughput
Abbelight SAFe-360. Multi-colour SMLM with high throughput. Best for screening many conditions or imaging multiple targets simultaneously.
Abbelight SOP →
Abbelight SOP →
Two channels, deeper into the sample, lower throughput acceptable
Abberior STED ExpertLine. STED gives you optical sectioning at moderate depth.
SOP coming soon.
SOP coming soon.
Single-molecule precision, simple labelling, easy operation
ONI NanoImager. Desktop SMLM, easy to learn, great for dSTORM with conventional dyes.
SOP coming soon.
SOP coming soon.
Yes, and I need higher resolution than fluorescence super-resolution can give
Beyond fluorescence super-resolution, electron microscopy resolves down to atomic scale. For non-living samples, consider SEM (surface morphology), TEM (thin sections, structural detail), or cryoTEM (vitrified biological samples). These are not at AMF; ICMS and TU/e host EM facilities, talk to an imaging scientist for a referral.
What next?
Found a likely match? Read the SOP, then book via Calira. First-time on the instrument? You’ll need a super-user introduction.