Nikon-Ti/ND-acquisition/Experiment-Design.md

+# Experiment Design (ND Acquisition)
+
+The ND acquisition tab let you combine the optical configurations you have saved into complex experiments.
+
+## Save Location 
+![](media/ND-aq1.png) 
+
+* Path      - location to save the file. It is convenient to save directly to mif_home.
+* File name - This is automatically incremented each time the acquisition is run.
+
+## Timelapse
+
+![](media/time-points-detail.png)
+
+1. Click on `Time` tab
+2. Add timing loops 
+
+You need to ensure that there is enough time to complete the combining multiple channels, Z-stacks and fields of view.  
+
+## XY points 
+
+### Manually adding points
+
+![](media/XY-points-detail.png)
+
+1. Check the `Include Z` box (this saves the focal plane)
+2. Move the stage with to new position.
+1. Click the `+` to add the current stage position.
+2. Points can deactivated by unchecking the boxes.
+3. Points can reordered by clicking the blue arrows
+
+Tips:
+
+* Click on the points to visit the location (`Move Stage to Selected Point` must be checked)
+* Select `Split Multipoints` under the `Advanced` if you a large numbers of point.  This makes importing and analysis easier.
+* Update the XY position for a point by clicking the `->`
+* Update the  Z position for a point by clicking the `<-` 
+* PFS offsets can saved for each point.
+* `Optimize` will reorder you points so that they are visited efficiently. 
+
+## Z-stack
+
+![](media/Z-stack-detail.png)
+
+## Multiple channels
+
+![](media/multi_channel-detail.png)
+
+1. Click `+` to add a channel
+2. Select the Optical Configuration from the drop down
+3. Channels can deactivated by unchecking them.
+4. Channels can reordered using the blue arrows
+