Part 1 Principles
1. Fluorescence microscope
2. Filterset in FL-Mic
3. How concocal differs?
4. What is confocal?
5. Resolution in confocal
6. Optical sectioning
7. Confocal image formation
    and time resolution
8. SNR in confocal
9. Variations of confocal
      microscope
10. Special features from
     Leica sp2 confocal
Part 2 Application
1. Introduction
2. Tomographic view
    (Microscopical CT)
3. Three-D reconstruction
4. Thick specimen
5. Physiological study
6. Fluorescence detecting
       General consideration
       Multi-channel detecting
       Background  correction
       Cross-talk correction
            Cross excitation
            Cross emission
            Unwanted FRET

Part 3 Operation and
             Optimization
 1. Getting started
 2. Settings in detail
      Laser line selection
      Laser intensity and 
         AOTF control
      Beam splitter
      PMT gain and offset 
      Scan speed
      Scan format, Zoom
        and Resolution
     Frame average, and
         Frame accumulation
     Pinhole and Z-resolution
     Emission collecting rang
        and Sequential scan

When Do you need confocal?
FAQ
Are you abusing confocal?

Confocal Microscopy tutorial

Part 2 application of confocal microscopy

3. 3-D reconstruction

Confocal Microscopy is the only way to get a true Z-stack for 3-D reconstruction from light microscope.

This is a gallery show of the total 40 optical sections taken from the whole length of the cell, top to bottom.

  The reconstructed 3-D model from the z-stacks:

This is the projection reconstructed from the 40 optical sections using averaging projection method. compare to any single image in the gallery, this reconstruction presents a much better view of the cell in the real space as 3 dimensional object.

  The Z-stack of optical sections can also be used to make a 3-D animation for viewing on the computer or over internet, or as a PowerPoint slide show. Bellowing is a gallery of the reconstructed video frames for showing a 3-D animation. The sections are taken  from the same Z-stacks as above.

This is the 3D-animation played from the frames showing in the gallery above.