Zeiss 800 Smilow 12
SN 2633000139

Advance scheduling:
http://signups.med.nyu.edu/facilities/equipment/signups/cancer-institute-confocal

Inverted microscope with AiryScan and environemental chamber, autofocus, and stage for multiposition time lapse.

Lenses:
63x/1.4 oil DIC Plan-Apochromat M27
40x/1.3 oil Iris (UV) VIS-IR Plan-Apochromat
20x/0.80 Plan-Apochromat M27
10x/0.30 EC Pla-Neofluar M27 (not recommended for confocal)
10x/0.45 PlanApochromat M27

Lasers:
405 nm
488
561
640

Detectors:
GaAsP
AiryScan (may be used as single detector)
GaAsP
ESID detector for transmitted imaging (requires laser set to high power)

Zen 2.1 (early version of Zen Blue which has vagaries different than Zen Black or newer versions of Zen Blue)
Cannot look at line sequectial tracks in live scan mode

If you need an explanation how to use the 63X lens to achieve full resolution, please ask Michael or Yan.
In brief:

• Pinhole 1 Airy unit (or smaller).
• Either increase the image size (number of pixels) or use Zoom to set pixel size to 0.1 um. 
• Slow scan or line average to reduce noise. (more info here)

General Confocal Best practices:

• The pinhole is what makes the confocal a confocal. 1AU (which means 1 Airy unit) or smaller (0.5 to 1.0 ok) and click the 1AU button each time you change lenses.
  If you are opening it for imaging fixed samples, you should go use a widefield fluorescence scope instead.
  Except in special case of live cell imaging where you understand that images are not confocal, this is NOT AN ACCEPTABLE WAY TO MAKE IMAGES BRIGHTER. You won't hurt the instrument, but when you write your methods, you won't be accurately describing your microscopy as "confocal".
• Offset. Always use at 0 or 1 (or greater than one in some rare cases).
  Negative numbers are wrong.
• Digital gain. The preset is 1. Leave it there.
• Zoom 1 or greater. Using a Zoom less than 1 may cause a hot spot &/or curvature at the edges.
• Avoid saturation. Saturating images 1.) makes features appear larger than they are, 2.) prevents quantification of intensities and 3.) may damage the detectors inthe microscope.
  Use the Range Indicator button to make sure you have no saturated pixels. If you see red pixels, you need to turn down the Gain or Laser.
  Turning gain down will reduce noise. Less noise means you can scan faster. (More here.)
• Always save images in .czi format. This preserves each channel and all instrument metadata.
  Why take images at high resolution of a confocal and then throw away this information by saving as lossy jpg?

Highly recommended reading: Tutorial: guidance for quantitative confocal microscopy

AiryScan:
Zeiss claims that the microscope is prealigned ideally.
However, we have found that AiryScan should be aligned at each imaging session because the prealignment does not match all samples.
Use single channel Continuous mode with small pixel size image and high speed and high zoom for alignment.
Pinhole is supposed to be 2.5 or so.
Instructions for Zeiss 880 version of AiryScan here.

760 nm SP filter installed 7 October 2019

LSM 800 Serial# 2633000139 which is currently located in Smilow 12.

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