Create confocal.md

Author: swharden

content/gear/confocal.md

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+---
+title: Confocal Microscope
+description: How to use the Nikon confocal microscope to image slides
+---
+
+{{< specific >}}
+
+## Nikon C2 Confocal Microscope
+* [Brochure](https://www.microscope.healthcare.nikon.com/products/confocal-microscopes/c2) (official)
+* [NIS-Elements Instructions](https://www.bu.edu/picf/files/2020/02/C2-Manual.pdf) (official)
+* [Operating Notes](https://apps.mnc.umn.edu/pub/equipment/nikon_confocal_sop.pdf) (University of Minnesota)
+* [Training Guide](https://dentistry.uth.edu/research/docs/c2%20-training-ppt-ut-dental.pdf) (UT Dental)
+* [NIS-Elements Basics](https://www.youtube.com/watch?v=JpsTn_Vz_U0) (YouTube)
+* [Imaging a Z-Stack](https://www.youtube.com/watch?v=IGPYkoZ1Bic) (YouTube)
+* Ramamurthy lab
+  * [Getting Started](https://www.youtube.com/watch?v=DsmMGmHEIJY)
+  * [Operating the Microscope Visually](https://www.youtube.com/watch?v=zHfRcDHhL9A)
+  * [???](https://www.youtube.com/watch?v=bkUS86MFjaU) (YouTube)
+  * [???](https://www.youtube.com/watch?v=SGcKHdiOi8Y) (YouTube)
+  * [???](https://www.youtube.com/watch?v=-xX0tFMMRxo) (YouTube)
+  * [???](https://www.youtube.com/watch?v=3PvtLlRFgQk) (YouTube)
+  * [How to clean oil from the objectives](https://www.youtube.com/watch?v=8_LclqI5zgI)
+
+## Startup
+* do not turn on nikon white light source
+* turn on sola fluorescent light source using power button on front
+* Turn on Nikon C2 using power button on front
+* Turn on laser switch on the back left by the power cord and turn key to ON
+* Turn on proscan by flipping the switch on the back right DOWN
+* open NIS elements software (select C2 confocal on startup)
+
+## Seeing fluorescent samples through the eyepiece
+* press "light" button to enable fluroescence light source
+* set path select knob on right of scope to "BINO"
+* rotate filter cubes to 2(UV/blue), 3 (blue/green) or 4 (green/red)
+* open the shutter on the front of the scope
+* use the coarse focus knob on the scope
+* use the joystick for fine focus and XY translation
+
+## Laser scanning confocal imaging
+* press "light" button to disable fluroescence light source
+* set path select knob on right of scope to "F"
+* open the shutter on the front of the scope
+* press "live" in the software
+
+## Objectives
+* 20x, 0.4 NA, air, 1.33 mm WD, [MRL00202](https://spectraservices.com/product/mrl00202.html)
+* 100x, 1.45 NA, oil, 0.13 mm WD, [MRD71970](https://spectraservices.com/product/mrd71970.html)