STARTUP AND SHUTDOWN INSTRUCTIONS FOR LEICA STELLARIS
as of 2025-10-01
A few rules:
Simple startup:
There are two imaging modes on this system. The one more like other confocals or a camera system is when the detectors are set for "intensity" or "digital." However, the Gain knob does not behave the way it does on older confocals. This is critical to understand.
We recommend using the photon counting mode which is the new Leica standard.
We highly recommend using the glow over LUT while imaging. This is the mode where the image looks orange and saturated pixels appear blue. This LUT allows you to see very dim or few counts pixels so you are less tempted to turn up the intensity. If there are also bright green pixels, these may be turned off.
If you have multiple conditions where intensity relationships are important or you are checking controls, you must start by setting intensity range for the brightest condition and leaving it there for all conditions. DO NOT SATURATE.
When taking tiled or mosaic images, beware the Task window in the lower right of the screen. This is your friend when you want to collect multiple regions automatically, but it is you enemy if you have multiple regions and you only want to collect one at a time. Before capturing the tiled region, be sure to only have the tasks you want executed checked. (And see below "Saving files")
Shutdown Turn off the system unless the next users it there waiting to use it or explicitly told you they are coming to use the system. It is your responsibility to make sure the system is turned off.
Saving files
Treat each project as a container for each sample or condition.
Name once. Files inside do not need to be named or could be called "Z series"
Each time switch samples, start a new project.
However, these files can get large, many GB. So may want to make a new project for the same sample to keep the file sizes low.
Also, issues of subdirectories within LIF files. These occur with tiling and FLIM. These do not cooperate well with importing into ImageJ, Imaris, etc.
Therefore, for tiled files, copy/paste or cut/move only the "merged" files to another project.
If you are comfortable that you only need the merged tiles file, you could delete the individual images from the project and only keep the merged files. (This will also halve the data size.)
For FLIM, we haven't worked out the details, but each run may be a different project.
Nobody is supposed to touch the keys on the system. If the lasers do not work, check if somebody disobeyed this rule.
If both moniotrs do not turn on, manually turn on with the power switch in back.
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Buttons on rear of display monitor. Vertical rectangle button at bottom is power. Turning this on should connect the monitor to the computer and automatically be recognized as a second screen. Four smaller square buttons are used for maneuvering through the sesstings menus. |
Monitors can be reporgrammed to turn on when power starts up:
1. Turn on the monitor.
2. Use monitor buttons positioned at the right back and make sure that the following settings are set: • Main Menu → Management → DDC/CI Support: OFF • Main Menu → Input Control → DP Hot-Plug Detection: Always Active
3. Turn the monitor off and on again. This ensures that the setting modifications are applied.
other notes...
LAX automatically initializes stage on startup, so no sample on the scope!
Top left of screen, Configuration, Turn on laser.
Gear Hardware, Bit Depth 16.
Highlight detector in slider to turn on /off in lower right
Add Laser, turn shutter on in tool with lines and bullets.
For MP and harmonics tracks, pinhole wide open.
For reflection imaging, look in AOBS settings.