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Nikon-Ti/parfocal/Parfocal_setup.md
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If the lenses have been setup to be parfocal then if focus is found on one objective, you kcna change it will be in-focus (or at least close) on another. This is usefule for find your sample.
### Setting up Parfocality # Setting up Parfocality
The focus was on histological slide for each lense and Z-position recorded There is big difference in the focal plane for the lenses, I’ve checked that they are all screwed in completely. Is this range normal?
| Lens | Z / um | |Mag | NA | | Imm | Pos | Working dist. | Z / um | website
|----------|---------| |-----|-----|----------------------|-----|-----|--- |----------|---------------------------------------------------------------------------------------------------|
| 20X | 2033.75 | | 20X | 0.45| Plan Fluor ELWD AD1 |Air | 1 | 8.2 – 6.9 | 2033.75 | [link](https://www.nikoninstruments.com/Product-Selectors/Objective-Comparison/\(items\)/i117)|
| 40X ELWD | 3304.38 | | 40X | 0.6 | S Plan Fluor |Air | 2 | 3.6 – 2.8 | 3304.38 |[link]( https://www.nikoninstruments.com/Product-Selectors/Objective-Comparison/\(items\)/i118) |
| 40X | 5265.08 | | 40X | 1.0 | Plan Apo |Oil | 3 | 0.16 | 5265.08 |[link](https://www.nikoninstruments.com/Products/Optics/Apochromat-Objectives/CFI-Plan-Apochromat-Series/CFI-Plan-Apochromat-Series-Specifications) |
| 60X | 2005.85 | | 60X | 0.95| Plan Apo |Air | 4 | 0.21 – 0.11 | 2005.85 |[link](https://www.nikoninstruments.com/Product-Selectors/Objective-Comparison/\(items\)/i99) |
| 100X | 2061.97 | |100X | 1.4 | Plan Apo VC |Oil | 5 | 0.13 | 2061.97 |[link](https://www.nikoninstruments.com/Product-Selectors/Objective-Comparison/\(items\)/i95) |
| 100X | 2055.35 | |100X | 1.45| Plan Apo 𝝺 |Oil | 6 | 0.13 | 2055.35 |[link](https://www.nikoninstruments.com/Product-Selectors/Objective-Comparison/\(items\)/i101) |
Following the instructions from page 84 the Nikon Eclipse Ti RCP manual the Auto-Link Function (ALF) was turned off and the ALF memory for each lens set at the focal points.
With ALF off when the lens is changed the lens is escaped to 500um, the turret rotated, and the lens is return to intial position. Following the instructions from page 84 the Nikon Eclipse Ti RCP manual:
1. the Auto-Link Function (ALF) was turned off the movements tab
2. the ALF memory for each lens set at the focal points and saved.
To test the setup I looked at the effect of swapping between lenses with ALF on and off. To illustrate the problem here is what happens when I change from 40X 1.0 (pos 3) to the 60X (pos 4).
| ALF status |Change to 60X | Z sequence |
|------------|---------------------|---------------------------------|
| OFF | side of Ti | 5290 -> 500 -> 5290
| OFF | RCP | 5290 -> 500 -> 5290
| OFF | software TiPad | 5290 -> 500 -> 5290 -> 2000
| | |
| ON | side of Ti | 5290 -> 500 -> 5290 -> 2000
| ON | RCP | 5290 -> 500 -> 5290 -> 2000
| ON | software TiPad | 5290 -> 500 -> 5290 -> 2000
#### ALF off sequence
1. the lens is escaped to 500um
2. the turret rotated
3. and the lens is returned to initial position.
#### ALF on sequence
1. the lens is escaped to 500um
2. the turret rotated
3. and the lens is return to initial position
4. lens shifted by the difference of the ALF memory Z heights.
##Issues
1. When the ALF is disabled from the RCP and the lenses are changed from from the software Ti Pad the ALF correction is being applied. This is not a major issue.
2. When the ALF is on, the lens is bought to the original Z position, then the corrected by the difference in ALF positions. This results in the lens ramming the sample for certain combinations (eg 40X 1.0 to 60X).
1. ALF Off on the RCP
Initial Focus with the 40X Z=5279
![ALF off](./media/ALF_off.mov)
a. Change to 60X with side of Ti Zf=5290
b. Change from RCP Zf=5290
c. Change from Software TiPad Z=5290, Zf=2000
2. ALF On:
a. 500, 5290, 2000