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docs:comparison_with_confocal [2015/08/04 16:19]
Jon Daniels 		docs:comparison_with_confocal [2016/05/09 23:18] (current)
Jon Daniels
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 The following comparison was written with diSPIM in mind, but the main points apply to all types of SPIM/LSFM. The following comparison was written with diSPIM in mind, but the main points apply to all types of SPIM/LSFM.
  
-Spinning disk confocal (SDCM) is just a massively parallel confocal implementation so it's faster but otherwise has the some characteristics as laser scanning confocal.+Spinning disk confocal (SDCM) is just a massively parallel confocal implementation so it's faster but otherwise has the same characteristics as laser scanning confocal.
  
-  * **Light dose:** Confocal has much more photobleaching/phototoxicity than SPIM (i.e. SPIM uses the excitation light much more efficiently).  Low light dose is the main motivation for most SPIM users.+  * **Light dose:** diSPIM has much lower dose and hence less photobleaching/phototoxicity than confocal. Reducing light dose is the main motivation for most SPIM users.
       * A rule of thumb is that you need X times as much light for confocal as you do for SPIM where X is the number of slices in your stack.       * A rule of thumb is that you need X times as much light for confocal as you do for SPIM where X is the number of slices in your stack.
       * [[http://www.nature.com/nbt/journal/v31/n11/fig_tab/nbt.2713_F3.html|Figure 3]] and [[http://www.nature.com/nbt/journal/v31/n11/fig_tab/nbt.2713_SV2.html|Supplementary Video 2]] of Wu et al. offer bleaching comparisons of imaging with diSPIM and SDCM.  Other papers such as [[http://dx.doi.org/10.1002/jbio.201200144|this one]] offer comparisons of light sheet with confocal which should apply to diSPIM.       * [[http://www.nature.com/nbt/journal/v31/n11/fig_tab/nbt.2713_F3.html|Figure 3]] and [[http://www.nature.com/nbt/journal/v31/n11/fig_tab/nbt.2713_SV2.html|Supplementary Video 2]] of Wu et al. offer bleaching comparisons of imaging with diSPIM and SDCM.  Other papers such as [[http://dx.doi.org/10.1002/jbio.201200144|this one]] offer comparisons of light sheet with confocal which should apply to diSPIM.
-  * **Z resolution:** diSPIM after registration/fusion has best Z-resolution.  Next best is confocal, which in turn has better Z resolution than single-view SPIM. +  * **Z resolution:** diSPIM after registration/fusion has best Z-resolution (same as XY resolution).  Next best is confocal, which in turn has better Z resolution than single-view SPIM. 
-      * Using Bessel beams to create the sheet can improve Z-resolution for single-view SPIM, but won't meaningfully change dual view resolution after registration/fusion.+      * Using Bessel beams to create the sheet can improve Z-resolution for single-view SPIM ("optical sectioning"), but won't meaningfully change dual view resolution after registration/fusion.
   * **XY resolution:** confocal and SPIM are comparable.   * **XY resolution:** confocal and SPIM are comparable.
-  * **Speed:** SPIM (per view) and SDCM have comparable speed (assuming SDCM has higher laser intensity to make up for the ~3% open area of the spinning disks). +  * **Speed:** SPIM (per view) and SDCM have comparable speed if SDCM laser intensity is increased to compensate for the ~3% open area of the disks. 
-      * Camera readout speed bounds the maximum achievable frame rate.  For example, 512 pixels high ROI is 2.5 ms readout time for sCMOS.  Allowing 2.5 ms illumination time results in 5 ms total per image or 200 frames per second.+      * Camera readout speed bounds the maximum achievable frame rate.  For example, 512 pixels high ROI is 2.5 ms readout time for sCMOS.  Allowing 2.5 ms illumination time results in 5 ms total per image or 200 frames per second.  Using a cylindrical lens instead of a scanned light sheet can reduce camera overhead.

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