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--- docs:manual [2019/01/18 20:03]
Melissa Glidewell switched to modular manual
+++ docs:manual [2019/03/11 16:37] (current)
Jon Daniels [Optical alignment]
@@ Line 4: / Line 4: @@
 ====== Overview ======
 {{section>modular_manual#overview&noheader}}
-The advantage of the diSPIM being dual-sided is that the role of the two objectives can be reversed to collect a second stack from a perpendicular direction. The two optical paths are usually symmetric, and are designated Path A and Path B. (The two paths are described in detail in the [[docs:mm_dispim_plugin_user_guide#diSPIM Plugin User Guide]].) Registration and joint deconvolution merge the two datasets for improved resolution isotropy.
+The core assembly, the SPIM head, can be mounted on various inverted microscopes. Thus far, microscope-specific adapter brackets((Attaching the SPIM precludes the use of the transmitted light optics because the brackets utilize the transmitted light pillar mounting point.)) exist for the following microscopes:
+  * ASI RAMM frame (<imgref SPIM_Figure>)
+  * Leica DMI-6000
+  * Nikon TE-300, Ti, TE-2000, Ti2
+  * Olympus IX-71/81, IX-73/83
+  * Zeiss Axio-Observer
 <imgcaption SPIM_Figure|Typical complete diSPIM system on RAMM frame showing major components. 1) SPIM-MOUNT , 2) SPIM-RAMM , 3) SPIM arm mount (RAO-0046 ), 4) piezo objective mover APZOBJ-200 or similar, 5) MIM inverted microscope with LS-50M stage, 6) CDZ-1000 centering stage or CDZ-R block, 7) LS-50M stage, 8) MIM-CUBE-II w/ mirror, 9) MIM-CUBE-II w/ fluorescence filters, 10) C60-TUBE_B imaging tube lens, 11) C60-TUBE_160 scanner tube lens, 12) 50mm extension tube, 13) MM-SCAN_1M light sheet scanner, 14) MS-2500 XY stage.>{{:docs:manual:dispim_figure.jpg?600| Typical complete diSPIM system on RAMM frame showing major components.}}</imgcaption>
@@ Line 11: / Line 17: @@
 The relevant sections of the diSPIM [[https://youtu.be/TAgbr6IrTqw|assembly]] video are embedded.
-===== Mount the SPIM Head =====
+===== SPIM Head =====
 {{section>modular_manual#mount_the_spim_head&noheader}}
 \\
@@ Line 20: / Line 26: @@
 \\
 <imgcaption SPIM_mount_to_RAMM| SPIM head mounts via 2 dowel pins and a bolt at the indicated location regardless of the microscope frame. (RAMM frame pictured)>{{:docs:manual/SPIM_mount_to_RAMM.png| The SPIM head mounted to the microscope frame via 2 dowel pins and a bolt.}}</imgcaption>
+===== Red Shipping Bracket =====
+{{section>modular_manual#red_bracket&noheader}}
 ===== Scanners =====
@@ Line 33: / Line 42: @@
 {{section>modular_manual#camera_setup&noheader}}
-==== Mount ====
+==== Mount Camera Tube Lenses ====
 Tools: M5 hex driver\\
-In the standard configuration for diSPIM on a RAMM frame, as in <imgref DiSPIM_Figure>, each camera tube lens is fastened to the SPIM-MOUNT((Other common configurations use a post mount system to minimize vibration from the camera's fans, or to accommodate an FTP system in lieu of a RAMM frame.)) with a ring clamp. The end of the tubes should come within approximately 1 mm from the upper (mirror) CUBE-IIIs. When the objectives are lowered into position for viewing a sample, adjust the bolts holding the tube support arms so the camera tube lenses are centered on the CUBE-IIIs. \\
+In the standard configuration for diSPIM on a RAMM frame, as in <imgref SPIM_Figure>, each camera tube lens is fastened to the SPIM-MOUNT((Other common configurations use a post mount system to minimize vibration from the camera's fans, or to accommodate an FTP system in lieu of a RAMM frame.)) with a ring clamp. The end of the tubes should come within approximately 1 mm from the upper (mirror) CUBE-IIIs. When the objectives are lowered into position for viewing a sample, adjust the bolts holding the tube support arms so the camera tube lenses are centered on the CUBE-IIIs. \\
 ==== Orient & Connect ====
@@ Line 53: / Line 62: @@
 If your system was delivered before 2015, refer to the document on [[hardware:dated#piezos|pre-2015 piezos]].
-The objective mounting assembly includes a lateral objective linear positioner (OBLPA) for one side of the SPIM head and a replacement spacer for the other, a piezo objective mover (POM), and the bushing that the objective screws into; see <imgref piezo_with_bushing>. The assembly mounts to the right angle bracket via dovetail joint and is secured into position via set screw.\\
+The objective mounting assembly includes a __ob__jective __l__ateral __p__ositioner __a__ssembly (OBLPA) for one side of the SPIM head and a replacement spacer for the other, a piezo objective mover (POM), and the bushing that the objective screws into; see <imgref piezo_with_bushing>. The assembly mounts to the right angle bracket via dovetail joint and is secured into position via set screw.\\
 <imgcaption piezo_with_bushing| Objective mounting assembly top to bottom: objective lateral positioner assembly (OBLPA), piezo objective mover (POM), bushing, objective>{{:docs:manual/piezo_with_bushing.jpg?300| Objective mounting assembly}}</imgcaption>
@@ Line 122: / Line 131: @@
-====== diSPIM Alignment ======
+====== Alignment ======
 The relevant sections of the diSPIM [[https://youtu.be/qnOrg30NNuE|alignment]] video are embedded.
@@ Line 150: / Line 159: @@
 ===== Optical alignment =====
+**Goals:**
+The qualities of final alignment (for both SPIM optical paths), include all of the following:
+  * beam/sheet plane coincident with imaging focus plane, near the center of the piezo and/or slice travel
+  * sheet centered in imaging camera field of view
+  * beam perpendicular to imaging camera field of view
+  * beam waist centered on imaging camera
+  * for dual view, epi spot centered on epi camera
+  * when mounted on an inverted microscope, sheets centered in bottom camera’s field of view (i.e. co-alignment of all three objectives)
+For single-view systems there are more adjustments than required to achieve good alignment of the single light sheet plane and detection focal plane and does not have an epi view. This makes it easier to align, but also makes it possible to adjust things so that the illumination is far from the center of the illumination objective so this should be checked by eye.
 ==== Overview ====
 {{section>modular_manual#alignment_overview&noheader}}
-Goals
-The qualities of final alignment, for both SPIM optical paths, include all of the following:
-epi spot centered on epi camera
-beam waist centered on imaging camera
-beam/sheet plane coincident with imaging focus plane near the center of the piezo travel
-beam perpendicular to imaging camera field of view
-sheet centered in imaging camera field of view
-sheets centered in bottom camera’s field of view (i.e. co-alignment of all three objectives)
-Exploring beam position and angle: what affects what?
 {{section>modular_manual#beam_position&noheader}}

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