Several microscopes are equiped with MicroFPGA together with Micro-Manager and htSMLM. In this section, we detail some aspect of our usage.
| Signal | Device | Electronics |
|---|---|---|
| Camera (in) | Photometrics Evolve 512 | SCB |
| Camera (in) | Hamamatsu ORCA-Flash4.0 V2, ORCA-Quest and ORCA-Fusion BT PCO edge 4.2 and 4.2bi Andor iXon Ultra 897 |
None |
| Camera (out) | Hamamatsu ORCA-Flash4.0 V2 | None |
| Laser trigger (out) | Toptica iChrome MLE and iBeamSmart Omicron LightHUB Oxxius LBX-405 Cobolt Jive 561 LaserQuantum gem 561 MPB Communications F-04306-107 and F-04-306-102 |
None |
| Laser trigger (out) PWM (out) |
Custom laser engine (link) | None |
| TTL (out) | LED switches | None |
| Servo (out) | Sail winch servos (e.g.: 1, 2 and 3) |
None |
| Analog (out): PWM + low-pass |
Omicron LH.AOM AA Opto-Electronic AA.AOTF.6C/TN |
SCB |
| TTL (out) | Owis KSHM 40 | None |
| Analog (in) | Focus stabilization (link) Laser powermeter (link) |
ACB |
SCB: signal conversion board (see electronics)
ACB: analog conversion board (see electronics)
The microscopes are controlled through Micro-Manager and a custom EMU plugin: htSMLM. Here is an overview of the mapping of the FPGA signals (device properties) in Micro-Manager to the htSMLM functionalities. Refer to the htSMLM guide for more details, in particular the descriptions of each panel.
| Signal | htSMLM panels |
|---|---|
| Laser trigger (mode, pulse duration, sequence) |
Laser trigger panels Activation laser panel Activation script panel |
| Servo | Filters panel Additional filters panel Controls panel |
| PWM | Laser control panels |
| TTL | Controls panel |
| Analog | QPD panel Powermeter panel |
MicroFPGA earlier versions have been used in the following publications (non-exhaustive list) and in most Ries lab (EMBL) projects:
- Deschamps, Joran, Andreas Rowald, and Jonas Ries. "Efficient homogeneous illumination and optical sectioning for quantitative single-molecule localization microscopy." Optics express 24.24 (2016): 28080-28090. link
- Schröder*, Daniel, Deschamps*, Joran et al. "Cost-efficient open source laser engine for microscopy." Biomedical optics express 11.2 (2020): 609-623. link
- Dasgupta*, Anindita, Deschamps*, Joran et al. "Direct supercritical angle localization microscopy for nanometer 3D superresolution." Nature communications 12.1 (2021): 1-9. link
- Mund, Markus, et al. "Superresolution microscopy reveals partial preassembly and subsequent bending of the clathrin coat during endocytosis." bioRxiv (2021). link
- Diekmann, Robin, et al. "Optimizing imaging speed and excitation intensity for single-molecule localization microscopy." Nature methods 17.9 (2020): 909-912. link
- Thevathasan, Jervis Vermal, et al. "Nuclear pores as versatile reference standards for quantitative superresolution microscopy." Nature methods 16.10 (2019): 1045-1053. link
- Mund, Markus, et al. "Systematic nanoscale analysis of endocytosis links efficient vesicle formation to patterned actin nucleation." Cell 174.4 (2018): 884-896. link