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docs:manual:alignment [2015/06/26 17:38]
Jon Daniels finished adding from lyx 		docs:manual:alignment [2020/08/19 02:50] (current)
Jon Daniels marked deprecated and linked to recent version
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-====== diSPIM Alignment ======+====== diSPIM Alignment (deprecated) ====== 
 + 
 +<note important>This is the original version of the manual and users should refer to [[docs:manual#optical_alignment|docs:manual#optical_alignment]] instead</note>
  
 ===== Overview ===== ===== Overview =====
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 ===== Beam position and angle: what affects what? ===== ===== Beam position and angle: what affects what? =====
  
-We are concerned with getting both the beam position and angle correct in the sample. Fortunately, the adjustments to do so are mostly “orthogonal” or independent of each other. The following table can be derived by understanding the lens system from the fiber input of the scanner to the sample and then through the imaging path to the corresponding camera on the opposite side of the microscope. <tabref what_affects_what> shows how various “knobs” affect the beam position and angle.+We are concerned with getting both the beam position and angle correct in the sample, plus making sure the objectives are looking at the same place. Fortunately, the adjustments to do so are mostly “orthogonal” or independent of each other. The following table can be derived by understanding the lens system from the fiber input of the scanner to the sample and then through the imaging path to the corresponding camera on the opposite side of the microscope. <tabref what_affects_what> shows how various “knobs” affect the beam position and angle.
  
 <tabcaption what_affects_what| How alignment adjustments affect the beam position and angle.> <tabcaption what_affects_what| How alignment adjustments affect the beam position and angle.>
 ^ Adjustment  ^ Position? ^ Angle? ^ Comments ^ ^ Adjustment  ^ Position? ^ Angle? ^ Comments ^
-| Tilt of dichroic mirror  | Some  | Yes | Position effect varies ((The dichroic tilt affects the angle at+| Tilt of dichroic mirror (Cube-III) | Some  | Yes | Position effect varies but usually small ((The dichroic tilt affects the angle at
 which the beam enters the back focal plane as well as the beam position at the back focal plane. It is possible to which the beam enters the back focal plane as well as the beam position at the back focal plane. It is possible to
 compensate by adjusting the scan center but we usually adjust the camera mirrors to compensate instead.)) | compensate by adjusting the scan center but we usually adjust the camera mirrors to compensate instead.)) |
-| Tilt of camera mirror  | Yes | No | Set during scanner alignment and not after | +| Tilt of camera mirror (Cube-III)  | Yes | No |  | 
-| Position of upper Z stage  | No | No | Angle varies if scanners are not connected to dichroic tubes | +| Z position of SPIM head relative to sample | No | No | | 
-| Tilt of adjustable mirror  | Some  | Yes | Set during scanner alignment and not after | +| Tilt of adjustable mirror (inside scanner) | Some  | Yes | Set during scanner alignment and not after, not user-adjustable | 
-| Tilt of main micro-mirror  | Yes| No | Set during scanner alignment and not after |+| Tilt of main micro-mirror (inside scanner)  | Yes| No | Set during scanner alignment and not after (not user-adjustable) |
 </tabcaption> </tabcaption>
  

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