Reading Assignments:

The Molecular Probes Handbook Fluorescence Fundamentals

Fluorescence microscopy – Lichtman & Conchello.pdf (or

Jablonski Diagram

Reading assignment: Jablonski Diagram.pdf

Ground state


Excited state

  • Collisional quenching
  • Fluorescence resonance energy transfer
  • Fluorescence excited-state lifetime

Inter system crossing to triplet state

  • Photobleaching
  • Photo activation


Molar extinction coefficient (e) or EC

Quantum Yield (QY)

Fluorescence intensity per dye molecule is proportional to EC X QY

Stokes Shift

Excitation Spectrum

Emission Spectrum

Fluorescence Excitation Sources

Reading Assignments:

Light Sources.pdf

Semrock – Optical Filters.pdf

Table 1: Lasers for popular fluorophores. “DPSS” = diode-pumped solid-state laser. “OPS” = optically pumped semiconductor laser.
“Doubled” = frequency doubled via a nonlinear optical crystal.

Fluorescence Filters

Reading assignment:

Optical Filters Handbook – Reichman.pdf (or

Fluorescence Detectors

Hamamatsu PMT handbook.pdf

Hamamatsu Cameras.pdf (or


Fluorescent Materials in Biology

Reading assignment:
The Fluorescent Toolbox.pdf (“The Fluorescent Toolbox” PMID: 16614209)

Fluorescent dyes

Fluorescent Proteins

Quantum Dots

Fluorescent Antibodies

[Zip Package of all Section 4 Documents]