Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision 		Previous revision
docs:modular_manual [2019/06/17 21:12]
Melissa Glidewell [Phase 1] 		docs:modular_manual [2022/10/25 22:47] (current)
Jon Daniels [Fine alignment]
Line 70: Line 70:
  
 <WRAP left round info 50%> <WRAP left round info 50%>
-Notice: It is very easy to warp dichroic mirrors; only lightly tighten the retaining clip of the D-CUBE.  +Notice: It is easy to warp dichroic mirrors enough to induce aberrations; only lightly tighten the retaining clip of the D-CUBE.  
 </WRAP> </WRAP>
 \\ \\ \\ \\ \\  \\ \\ \\ \\ \\ 
Line 186: Line 186:
  
 ===== Beam position ===== ===== Beam position =====
-We are concerned with getting both the beam position and angle correct. Fortunately, the adjustments to do so are mostly independent of each other. <tabref what_affects_what> can be derived by understanding the light path.\\ +We are concerned with getting both the beam position and angle correct, along with getting both objectives "looking" at the same place. Fortunately, the adjustments to do so are mostly independent of each other. <tabref what_affects_what> can be derived by understanding the light path.\\ 
  
 <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 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.))  | +| Tilt of dichroic mirror (Cube-III)              | Some             | Yes             | Position effect 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 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              | Set during scanner alignment and not after                                                                                                                                                                                                                                                    | 
-| Position of upper Z stage             | No               | No              | Angle varies if scanners are not connected to dichroic tubes                                                                                                                                                                                                                                  |+| Z position of SPIM head             | No               | No              |                                                                                                                                                                                                                                   |
 | Objective bushing (focus)             | Maybe minor      | Maybe minor     | If the bushing isn't perfectly concentric then slight movements can occur but this isn't usually a problem                                                                                                                                                                                    | | Objective bushing (focus)             | Maybe minor      | Maybe minor     | If the bushing isn't perfectly concentric then slight movements can occur but this isn't usually a problem                                                                                                                                                                                    |
 | Linear objective adjustment           | Yes              | Maybe minor     |                                                                                                                                                                                                                                                                                               | | Linear objective adjustment           | Yes              | Maybe minor     |                                                                                                                                                                                                                                                                                               |
-| <del>Tilt of adjustable mirror</del>  | <del>Some</del>  | <del>Yes</del>  | <del>Set during scanner alignment and not after</del>                                                                                                                                                                                                                                         | +| <del>Tilt of adjustable mirror</del>  | <del>Some</del>  | <del>Yes</del>  | <del>Set during scanner alignment, not user-adjustable</del>                                                                                                                                                                                                                                         | 
-| <del>Tilt of main micro-mirror</del>  | <del>Yes</del>   | <del>No</del>   | <del>Set during scanner alignment and not after</del>                                                                                                                                                                                                                                         |+| <del>Tilt of main micro-mirror</del>  | <del>Yes</del>   | <del>No</del>   | <del>Set during scanner alignment, not user-adjustable</del>                                                                                                                                                                                                                                         |
 </tabcaption> </tabcaption>
  
Line 248: Line 248:
  
 **Outline**\\  **Outline**\\ 
 +  * Phase 0 (coarse alignment by eye as described above)
   * Phase 1 (iterative)   * Phase 1 (iterative)
-    * 1. Co-align SPIM objectives to focus and center beams. +    * 1.1 Co-align SPIM objectives to focus and center beams. 
-    * 2. Tilt dichroic mirrors for horizontal beams __uniformly__ in/out of focus.  +    * 1.2 Tilt dichroic mirrors for __horizontal__ beams __uniformly__ in/out of focus.  
-    * 3. Tilt imaging mirrors to center epi spots.+    * 1.3 Tilt imaging mirrors to center epi spots. 
 +    * 1.4 Adjust lateral position of objective. 
 +    * 1.5 Go back to 1.1 and repeat until no adjustments needed
   * Phase 2 (may have to be repeated for initial alignment, and again when scanners or cameras are changed or disturbed)   * Phase 2 (may have to be repeated for initial alignment, and again when scanners or cameras are changed or disturbed)
-    * 4. Focus collimators to center beam waists in FOV. +    * 2.1 Focus collimators to center beam waists in FOV. 
-    * 5. Rotate scanners for __uniform__ focus of the sheets. +    * 2.2 Rotate scanners for __uniform__ focus across the sheets. 
-    * 6. Rotate cameras for vertical sheets from epi view. +    * 2.3 Rotate cameras for vertical sheets from epi view. 
-  * Phase 3 (performed just once for initial alignment and again for objective or sample changes) +    * Go back to 1.1 
-    * 7. Establish the coverslip location. +  * Phase 3 (performed just once for initial alignment and again for objective change) 
-    * 8. Align the inverted scope with the SPIM objectives. +    * 3.1 Establish the coverslip location. 
-    * 9. Cross-calibrate the piezo and light sheet movement.+    * 3.2 Align the inverted scope with the SPIM objectives. 
 +    * 3.3 Cross-calibrate the piezo and light sheet movement. 
 +  * Phase 4 (performed for any new sample)  
 +    * 4.1 Check that light sheet and detection plane are coincident; adjust offset in plugin if needed.
  
 ==== Phase 1 ==== ==== Phase 1 ====

Trace: