Instruments/Zeiss-Elyra-7.md

@@ -18,42 +18,65 @@ Use a yellow marker pen slide with a coverslip and a slide with beads (100nm Tet
 
 1. With the 10x objective (no oil) focus on the marker pen slide
 2. Image Setup for camera 2 (TV2) calibration: lattice SIM, LBF 405/488/561/642, LP560, use the biggest (42µm) grid
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+![Imaging_Setup](uploads/be514fceb9bde8b03521a6bd21101694/Imaging_Setup.jpg){width=75%}
+
 3. Focus on the lattice pattern and take a ‘Snap’
 4. Go to ‘Graphics’ and draw an arrow/line across the pattern
 
-![Graphics](uploads/a5c85c9914eee4c16a20224af2c69ba5/Graphics.jpg)
-![Grid](uploads/a1e938d78726d18e1c3285c271ab996e/Grid.jpg)
+![Graphics](uploads/a5c85c9914eee4c16a20224af2c69ba5/Graphics.jpg){width=75%}
+![Grid](uploads/a1e938d78726d18e1c3285c271ab996e/Grid.jpg){width=75%}
 
 5. Make sure that the ends of the arrow are placed in the same line across the image, switch off the interpolation
 
-![Grid_left](uploads/a87bec7600fdf31fe9b0065a2f23a0f4/Grid_left.jpg)![Grid_right](uploads/662b603921d038da3c9954f49d771493/Grid_right.jpg)![Dimensions](uploads/b3c918277fc692ab3a6e923208c0dc5a/Dimensions.jpg)
+![Grid_left](uploads/a87bec7600fdf31fe9b0065a2f23a0f4/Grid_left.jpg){width=75%}![Grid_right](uploads/662b603921d038da3c9954f49d771493/Grid_right.jpg){width=75%}![Dimensions](uploads/b3c918277fc692ab3a6e923208c0dc5a/Dimensions.jpg){width=75%}
 
 6. In ‘Graphics’ activate ‘M’ (measurement) and check the angle 
 
-![Graphics_measure](uploads/8de9fc67bee34262465186b8022c2c1f/Graphics_measure.jpg)![Grid_angle](uploads/fbea05bb3dba5378465ed6d94f36d71a/Grid_angle.jpg)
+![Graphics_measure](uploads/8de9fc67bee34262465186b8022c2c1f/Graphics_measure.jpg)![Grid_angle](uploads/fbea05bb3dba5378465ed6d94f36d71a/Grid_angle.jpg){width=75%}
 
 7. Go to ‘Maintain’, and drag out the ‘Dual Camera Adapter Alignment’ tool
 
-![Maintain](uploads/4cd5fe821496c21336794064bfb57643/Maintain.jpg)
+![Maintain](uploads/4cd5fe821496c21336794064bfb57643/Maintain.jpg){width=75%}
 
 8. Tick 'Calibration pattern'
-8. Change the ‘Rot [°]’ value. Take another snap of the marker sample and measure the angle again, change the ‘Rot [°]’ value again. Repeat until you measure a value lower than 0.05°. Store current position in the ‘Dual Camera Alignment’ tool
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+![Dual_camera_adapter_alignment_Rotation](uploads/412a55c368749394293a088ec4cd79a4/Dual_camera_adapter_alignment_Rotation.jpg){width=75%}
+
+8. Change the ‘Rot [°]’ value. 
+9. Untick 'Calibration pattern'
+10. Take another snap of the marker sample and measure the angle again, change the ‘Rot [°]’ value again. Repeat until you measure a value lower than 0.05°. Store current position in the ‘Dual Camera Alignment’ tool
 
 ### Camera xyz-Alignment
 
-9. Change to 63x 1.4 (SIM) or 1.46 (TIRF) objective, use the bead slide and focus on beads. Use the same imaging method that you will use for your experiment (LASER WF, SIM, Apotome etc.)! In 'Acquisition' set up the 561nm laser for camera 1 (TV1) and the green laser for camera 2 (TV2) with exposure time 100ms and 1-5% of the laserpower (>1000 white/grey values!). If working in multitrack always keep track 1 with camera 2! Choose the optimal grid pattern.
+9. Change to 63x 1.4 (SIM) or 1.46 (TIRF) objective, use the bead slide and focus on beads. Use the same imaging method that you will use for your experiment (LASER WF, SIM, Apotome etc.)! In 'Acquisition' set up the 561nm laser for camera 1 (TV1) and the green laser for camera 2 (TV2) with exposure time 100ms and 1-5% of the laserpower (>1000 white/grey values!). Always keep track 1 with camera 2! Choose the optimal grid pattern.
 10. Go to 'Continuous' and focus through the beads. The optimal focus (smallest diameter of the bead) should be the same for both color channels. If not:
 11. Go to ‘Maintain’, and drag out the ‘Dual Camera Adapter Alignment’ tool
+
+![Dual_camera_adapter_alignment_z](uploads/baf459b3665bf0259ac6862e6041fa23/Dual_camera_adapter_alignment_z.jpg)
+
 12. Change the Z value until good overlap of the channels is achieved. Focus up and down, and change the Z value until the beads are perfectly in focus for both channels simultaneously.
 13. Take a small Z-stack (20 slices) using optimal sampling, SIM process Z-Stack in case of SIM (no processing in case of TIRF or WF)
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+![z_Stack](uploads/fdd2862a0cfb692cfa79a54091351401/z_Stack.jpg)
+
 14. Go to orthogonal View and, in Dual Camera Adapter Alignment tool, fine-tune the Z value if necessary. Larger Z values correspond to a shit of the green channel to the left. Then, acquire another Z-stack until perfect overlap of channels is achieved. Store current position! 
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+![Ortho_view](uploads/6019434e0cb0d148dd85d0c02a10e5b8/Ortho_view.jpg){width=75%}
+
 15. In Dual Camera Adapter Alignment tool click XY for automatic alignment, if good overlap of channels is achieved, store current position, if not – move to stored position and in 'Continuous' mode change X and Y in the Dual Camera Adapter Alignment tool until overlap is achieved. Especially the beads in the center of the field of view should nicely overlap. Use the 'Profile > Display > Marker > Difference' tool to check the overlap.
+
+![Dual_camera_adapter_alignment_xy](uploads/1224a127963f3b439bf0547942ef9375/Dual_camera_adapter_alignment_xy.jpg){width=75%}![beads_xy](uploads/78d4f493776d040aacaddeff9ff0b495/beads_xy.jpg){width=75%}
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 16. Tick 'Calibration pattern' and check XY Overlap. Store current position!
 
 ### Channel Alignment
 1. Change to 63x 1.4 (SIM) or 1.46 (TIRF) objective, use your own bead slide, and focus on beads
 2. Take a large Z-stack (50 slices) using optimal sampling
 3. Go to processing – Channel alignment
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+![Channel_alignment](uploads/c417b9e33f81c34e0d7237a3b287892c/Channel_alignment.jpg){width=75%}
+
 4. Choose the input image, activate Fit and Affine, Click apply
 5. Save the results in order to correct your images later on.