LSM 900 upright confocal microscope  SB 12 32

All use must be scheduled in advance. If you walk-in to use the instrument, please immediately enter this in the scheduling system before starting up the software.
https://nyulangonesignups.resourcescheduler.net/resourcescheduler/schedule.asp?Topic=RES&TopicId=243

Instrument specifications:

• Axio Imager Z2 upright microscope system
• 3 GaAsP Detectors
• 4 diode lasers (405, 488, 561, 640nm)
• ESID Electronically switchable illumination and detection module for transmitted light
• Epi Illumination 4 color LEDs for visualization at the eyepieces
• Motorized XY scanning stage with mounts for slides
• 10x/0.45 air, 20x/0.8 air, 40x/1.4 oil & 63x/1.4 oil objectives
• Workstation with 32" Monitor
• ZEN software with Tiles and Positions, Z-Stacking, Time Lapse, Image Analysis, Colocalization, 3D Rendering, Spectral Unmixing, Smart Acquisition and more
• Air table
• Zeiss Predictive Service

The 40X/1.4 lens has the same resolution as the 63x/1.4 lens, but with a larger field of view.  For the highest resolution largest fields of view, increase the image size pixel dimensions until  the pixel size is what you consider highest resolution, e.g. 0.10 um.  The software has automated reporting for what Zeiss considers best resolution.

How to turn on:   Order of these switches does not matter.

• Two power switches on box to left of table.
• Computer.
• Wait for touch pad on microscope to turn on before running Zen software.

   The previous Zeiss 800 had an additional power strip.    Do not touch the power strip on this system. 

Data Storage - Always copy your data to a remove server; there is no guarrantee that data stored on this computer will be preserved.

• Save all files in .czi format
• Save all files on drive D:
• NO DATA STORED ON DESKTOP, drive C:, Documents, Pictures, etc.
• To transfer files to research-cifs, use the shortcut
   
  Enter nyumc\yourKID

How to turn off:

• Quit Zen.
• Wait for the white window which pops up to say that the software has quit completely.
• Two power switches on box to left of table.
• Log out or shut down computer.

Sample Prep

Lenses will crash into the microscope stage if the sample is too close to the end of the slide!
Use #1.5 coverslips (unless you have a specific reason for doing otherwise) and make sure anything you need to image is further than 5 mm from the end of the slide.

Do not put samples too close to the end of the slide.

If the samples (what you want to image) are too close to the end of the slide, then the lens will crash into the stage. This happens with both upright and inverted microscopes.

If the lens gets too close to the stage, it will crash into the stage, and this would damage the lens &/or bend the stage.

Therefore, samples cannot be imaged if they are too close to the end of the slide.  Anything you need to image must be more the 5 mm from the end of the slide.

Do not move the lens closer to the edge of the sample than pictured here.

Basic imaging quality control

Do not saturate images.

Always leave the Digital Offset at 0 and the Digital Gain at 1.
DO NOT use these to reduce background or brighten the image. Especially if you want to do intensity quantification later, using these will complicate or nullify the ability to do so.