References & image credits

This simulation teaches generic microscopy principles. Its optics, noise, timing and dose are simplified teaching models, not a calibration or operating procedure for a real instrument. Reference links are optional reading; their inclusion does not imply endorsement.

Scientific principles

• Infinity-corrected image formation: Nikon MicroscopyU · Infinity Optical Systems ↗
• Resolution and numerical aperture: Nikon MicroscopyU · Resolution ↗
• Köhler illumination: Nikon MicroscopyU · Conjugate Planes ↗
• Fluorescence light path: Nikon MicroscopyU · Introduction to Fluorescence Microscopy ↗
• Confocal acquisition: Nikon MicroscopyU · Critical Aspects of Confocal Microscopy ↗
• Photon noise: Hamamatsu · Calculating SNR ↗

Recorded cells

Allen Institute for Cell Science, via scikit-image, CC0. The volume has 60 planes and two recorded channels: membranes and nuclei. Source sampling is 0.26 µm in XY and 0.29 µm in Z; scikit-image’s rendition was downsampled fourfold in XY.

The simulator preserves that rendition’s voxels, then applies teaching colours and simulated blur, projection, illumination and detector effects. Simulated counts are not the original photon measurements. Zoom cannot recover detail absent from the source.

Dataset and sampling ↗ · Archived CC0 record ↗ · File-specific Allen confirmation, 13 January 2022 ↗

Recorded skin

H&E skin image by Kilbad, Wikimedia Commons, via scikit-image, public domain. The 1280 × 960 source rendition was centrally cropped to 960 × 960 and resized to 512 × 512 with Lanczos resampling.

This is one recorded plane with unknown physical pixel size. Focus adds simulated blur; no measured scale bar or recorded Z volume is implied.

Image and public-domain dedication ↗ · Pinned source record ↗

Synthetic images and drawings

The synthetic cells, beads and stained-section phantom, generic microscope stand and icon are original procedural teaching assets, declared CC0 by this project. Scientific articles explain their principles; they are not the source of these generated image pixels.

What the model simplifies

Rays, movement and instrument geometry are schematic. Optical estimates and sampling guides are idealized. Pinhole response, filter curves, detector response, bleaching and damage thresholds are not instrument-calibrated. The model does not quantitatively reproduce aperture-dependent depth of field or a full photon budget across changes in zoom.

Exercises use disclosed teaching criteria. A pass is practice feedback, not certification of microscopy skill. The independent experiment records reflection for human review; it does not automatically assess the scientific accuracy of that writing.

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