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feat: add laser channels; use them in the confocal examples and docs - #164
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- `LASER_405/445/488/515/561/640` library channels: a laser, a dichroic (main beam splitter) and an emission bandpass. `power` is the peak irradiance at the focus (1e5 W/cm^2 is ~50 uW at NA 1.4). - confocal examples, notebooks and docs use laser lines, HyD detectors and realistic powers and pixel dwell times, rather than broadband filter cubes (and mostly real fluorophores rather than the mock one). - re-executed the tutorial and example notebooks, without log output. - the README example uses a 0.6 AU pinhole (0.2 AU was very photon-starved). - `fpbase_scope.py` uses widefield (its filter set is a widefield cube). - README and docs/index.md now fetch EGFP from FPbase, so their doc tests are skipped offline. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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- the README and quickstart go back to the defaults-only example (with a 1 AU pinhole), and the docs get a separate "more realistic confocal" example with EGFP, LASER_488, a HyD and a 2 us dwell. - `LASER_*` channels default to `power=1e5` (W/cm^2 peak at the focus, ~50 uW at NA 1.4), so they give a sensible image without setting it. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Follow-up to #163. This adds
LASER_405,LASER_445,LASER_488,LASER_515,LASER_561andLASER_640tomicrosim.schema.optical_config.lib: a laser line, a dichroic (main beam splitter) and an emission bandpass. The filters are generic (not specific products).powerdefaults to 1e5 W/cm² (peak irradiance at the focus... about 50 µW at NA 1.4), so they work out of the box:Now that confocal actually computes excitation at the excitation wavelength, it felt pretty wrong for all of our confocal examples to be using broadband widefield filter cubes with the mock fluorophore and a CCD. So the confocal examples, docs and notebooks now use laser lines, a HyD detector, and realistic pixel dwell times (a few µs). A few other things along the way:
fpbase_scope.pynow uses widefield, since its filter set is a widefield cubedocs/index.mdnow fetches EGFP from FPbase, so that doc test is skipped when offline (likestages.mdalready was)Smarter defaults for
Confocal()(e.g. a laser channel rather than the FITC cube when you don't passchannels) would be nice too, but I'll leave that for a follow-up.