Instruments/Zeiss-Elyra-7.md

@@ -39,7 +39,7 @@ Camera Alignment has to be checked/done before **each experiment** using both ca
 
 ### Camera Rotation
 
-Use the yellow marker pen slide with a coverslip (on the desk next to the lens cleaning paper) and the slide with beads (multispec low, they are stored in the fridge's door close to the Elyra).
+Use the yellow marker pen slide with a coverslip (on the desk next to the lens cleaning paper) and the slide with beads (multispec low, they are stored in the fridge close to the Elyra).
 
 ![PXL_20240321_131615341](uploads/9c0a3a7f70adb315ded4ebd63222571c/PXL_20240321_131615341.jpg){width=40%} ![PXL_20240321_131830944](uploads/8fb5c5277bf0106adaef969aefefa79d/PXL_20240321_131830944.jpg){width=40%}  
 
@@ -99,11 +99,14 @@ Use the yellow marker pen slide with a coverslip (on the desk next to the lens c
 ![alignment_perfect](uploads/aa812ef246b98650bcd219c65a3c7b2f/alignment_perfect.PNG)
 
 ### Channel Alignment
+
+Channel Alignment has to be done before **each colocalization experiment** using multiple color channels and for **each used filter** in the camera link, for **each used objective** and for **each configuration of different cameras/tracks** individually. A bead sample has to be prepared by the user beforehand, the exact same way (same mounting etc.) as the actual sample. If your lab does not have beads, contact the facility staff and they will show you which ones to purchase (Tetraspeck 100nm beads, they are stored in the fridge's door close to the Elyra).
+
 1. Use the 63x 1.4 (SIM) or 1.46 (TIRF) objective, use your own bead slide, and focus on beads. Use the same filters as for your experiment and set up the cameras and tracks the same way as you will use them in your experiment. Set the illumination time to 100ms and use 0.1-1% laser power (when pressing min/max you should have >1000 white/grey values, when ticking 'Show all' in the 'Display' panel). Use the optimal grid pattern.
 2. Take a large Z-stack (50 slices) using optimal sampling (double-click on [Opt])
 3. Go to Processing – Channel alignment
 
-![Channel_alignment](uploads/17ba46853b6143467d8f1913ca8a3b5b/Channel_alignment.jpg)
+![Channel_alignment](uploads/17ba46853b6143467d8f1913ca8a3b5b/Channel_alignment.jpg){width=50%}
 
 4. Choose the input image, activate Fit and Affine, Click apply
 5. Save the results in order to correct your images later on