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 [2019/02/27 23:08]
Melissa Glidewell [Orientation] 		docs:modular_manual [2022/10/25 22:47] (current)
Jon Daniels [Fine alignment]
Line 8: Line 8:
 ===== Mount the SPIM Head ===== ===== Mount the SPIM Head =====
 {{ youtube>TAgbr6IrTqw?start=215&end=377&rel=0&small}}  {{ youtube>TAgbr6IrTqw?start=215&end=377&rel=0&small}} 
-**Tools**: M6 hex driver\\ +**Tools**: 6 mm hex driver\\ 
 The video is cued up to show the process for mounting a diSPIM onto an ASI RAMM frame, but the principles apply to other scopes as well.\\  The video is cued up to show the process for mounting a diSPIM onto an ASI RAMM frame, but the principles apply to other scopes as well.\\ 
  
Line 18: Line 18:
  
 ===== Red Bracket ===== ===== Red Bracket =====
-**Tools**: M5 and M6 hex drivers\\ +**Tools**: 5 mm and 6 mm hex drivers\\ 
  
 RAMM frames are shipped with a red bracket supporting the inverted scope; it must be removed. For detailed instructions with pictures, please visit [[http://asiimaging.com/docs/removing_red_shipping_bracket|ASI's documentation site]]. RAMM frames are shipped with a red bracket supporting the inverted scope; it must be removed. For detailed instructions with pictures, please visit [[http://asiimaging.com/docs/removing_red_shipping_bracket|ASI's documentation site]].
Line 27: Line 27:
 ===== Scanners ===== ===== Scanners =====
 {{ youtube>TAgbr6IrTqw?start=480&end=697&rel=0?small}} {{ youtube>TAgbr6IrTqw?start=480&end=697&rel=0?small}}
-**Tools**: M2 hex driver\\ +**Tools**: 2 mm hex driver\\ 
 The video is cued up to show the process for mounting the scanners.\\  The video is cued up to show the process for mounting the scanners.\\ 
  
Line 36: Line 36:
 ===== Orientation ===== ===== Orientation =====
 {{ youtube>TAgbr6IrTqw?start=695&end=878&rel=0?small}}  {{ youtube>TAgbr6IrTqw?start=695&end=878&rel=0?small}} 
-**Tools**: M2 hex driver\\ +**Tools**: 2 mm hex driver\\ 
 The video is cued up to show the process for mounting and orienting the cameras.\\  The video is cued up to show the process for mounting and orienting the cameras.\\ 
  
Line 64: Line 64:
 ===== Filters and Mirrors ===== ===== Filters and Mirrors =====
 {{ youtube>TAgbr6IrTqw?start=1251&end=1721&rel=0?small}} {{ youtube>TAgbr6IrTqw?start=1251&end=1721&rel=0?small}}
-**Tools**: ASI ring tool, small Phillips head screwdriver, M2 hex driver\\ +**Tools**: ASI ring tool, small Phillips head screwdriver, 2 mm hex driver\\ 
 The video is cued up to show the process for installing an excitation filter, emission filter, and dichroic filter.\\  The video is cued up to show the process for installing an excitation filter, emission filter, and dichroic filter.\\ 
  
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 106: Line 106:
  
 ===== Stage limits ===== ===== Stage limits =====
-**Tools**: M1.5 hex driver\\ +**Tools**: 1.5 mm hex driver\\ 
  
 Setting the limit magnets on the motorized stages prevents crashes that can break coverslips or otherwise damage equipment; hardware limits are the most foolproof way to prevent crashes.((Limits may also be defined in software. Software-defined limits persist when the controller is powered down, but are lost when the firmware is updated or reset.)) The limit magnets move with the stage plates; when a magnet approaches a Hall effect sensor affixed in the stage body, the firmware detects a limit condition and stops the stage. The polarity of limit magnets relative to the stage is essential to their function.  Setting the limit magnets on the motorized stages prevents crashes that can break coverslips or otherwise damage equipment; hardware limits are the most foolproof way to prevent crashes.((Limits may also be defined in software. Software-defined limits persist when the controller is powered down, but are lost when the firmware is updated or reset.)) The limit magnets move with the stage plates; when a magnet approaches a Hall effect sensor affixed in the stage body, the firmware detects a limit condition and stops the stage. The polarity of limit magnets relative to the stage is essential to their function. 
Line 116: Line 116:
  
 ===== Single axis =====  ===== Single axis ===== 
-{{ youtube>qnOrg30NNuE?start=952&end=1217&rel=0?small}}**Tools**: M1.5 hex driver\\ +{{ youtube>qnOrg30NNuE?start=952&end=1217&rel=0?small}}**Tools**: 1.5 mm hex driver\\ 
 The video is cued up to demonstrate setting the F-axis limit magnet.\\  The video is cued up to demonstrate setting the F-axis limit magnet.\\ 
  
Line 157: Line 157:
 ===== XY-axes ===== ===== XY-axes =====
 {{ youtube>qnOrg30NNuE?start=952&end=1217&rel=0?small}} {{ youtube>qnOrg30NNuE?start=952&end=1217&rel=0?small}}
-**Tools**: M1.5 hex driver\\ +**Tools**: 1.5 mm hex driver\\ 
 The video is cued up to demonstrate setting the XY-axes limit magnets; note that we now recommend setting the X-axis magnets first.\\ The video is cued up to demonstrate setting the XY-axes limit magnets; note that we now recommend setting the X-axis magnets first.\\
  
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 ====
-Repeat the steps of Phase 1 steps multiple times (after the first iteration, in no particular order) as you spiral in on alignment.+Repeat the steps of Phase 1 steps multiple times as you spiral in on alignment.
  
 === Cofocus SPIM objectives === === Cofocus SPIM objectives ===
 {{ youtube>qnOrg30NNuE?start=1694&end=2379&rel=0?small}} {{ youtube>qnOrg30NNuE?start=1694&end=2379&rel=0?small}}
-**Adjust**: OBLPA (<imgref piezo_with_bushing>) for steering the beams up and down in the Live mode window((i.e. aligning the beams in the Y-axis)) and threaded objective bushings for focusing\\  +**Configure** the [[docs:mm_dispim_plugin_user_guide#setup_path_tabs|Setup Path tabs]]:\\ 
-**End goal**: Both beams in focus with the epi-spot sitting on the beam waist (roughly at first, as in <imgref BeginAlign>, but better and better in subsequent iterations of Phase 1, as in <imgref ImprovingAlign>)\\  +select the checkboxes for 1) the "excitation beam" and 2) "Change settings on tab activate", and\\  
-The video is cued up to demonstrate cofocusing the SPIM objectives using Micro-Manager.\\+use the "On tab activate" drop down menu to select the Imaging camera.
  
-In the [[docs:mm_dispim_plugin_user_guide#navigation_tab|Navigation tab]], select the checkboxes for both Path A beam and Path B beam, and click on the **Multi** (for Multi camera overlay) and **Live** buttons.+**Adjust**: 
 +  * both objective bushings, and  
 +  * the knob on the OBLPA (<imgref piezo_with_bushing>) to center the beams in the Live window ((This aligns the beams in the Y-axis.))\\  
 +**The goal** is to have both beams in focus (roughly at first, as in <imgref BeginAlign>, but better and better in subsequent iterations of Phase 1, as in <imgref ImprovingAlign>).\\  
 +The video is cued up to demonstrate cofocusing the SPIM objectives using Micro-Manager.\\
  
 This is best done by alternating between steering and focus adjustments, alternating sides, __moving halfway to focus at a time__  until both beams are centered and focused. (See the [[hardware:troubleshooting#lack_of_bushing_travel|troubleshooting]] page if you cannot focus for lack of bushing travel.) Keep in mind that the nominal spacing between the objective bushing and piezo is 1 mm as pictured in <imgref piezo_with_bushing>. This is best done by alternating between steering and focus adjustments, alternating sides, __moving halfway to focus at a time__  until both beams are centered and focused. (See the [[hardware:troubleshooting#lack_of_bushing_travel|troubleshooting]] page if you cannot focus for lack of bushing travel.) Keep in mind that the nominal spacing between the objective bushing and piezo is 1 mm as pictured in <imgref piezo_with_bushing>.
Line 347: Line 357:
 **Adjust**: Rotation of the camera (and camera's tube lens)\\  **Adjust**: Rotation of the camera (and camera's tube lens)\\ 
 **End goal**: Epi-view of the sheets produces a vertical line in the camera image\\  **End goal**: Epi-view of the sheets produces a vertical line in the camera image\\ 
-**Tools**: M5 hex driver+**Tools**: 2 mm hex driver
 The video is cued up to demonstrate adjustment of the camera's rotation.\\  The video is cued up to demonstrate adjustment of the camera's rotation.\\ 
  
-If the epi-view of the sheet is not vertical, adjust the camera via its tube lens (loosen the two bolts in the wide split ring holding the camera tube lens until the tube lens will rotate). Because we already verified the scanner orientation, any remaining tilt must be in the camera. Rotate as needed and tighten the bolts. Check both cameras. +If the epi-view of the sheet is not vertical, slightly loosen the set screws holding the camera's C-mount adapter to the tube lens, rotate the camera/adapter as needed, and retighten the screws. Because we already verified the scanner orientation, any remaining tilt must be in the camera. Check both cameras. 
  
 If you make any changes in Phase 2, return to the start of Phase 1. If you make any changes in Phase 2, return to the start of Phase 1.

Trace: