Introduction protocol
Based on Hänsch, Sebastian 27.11.2018
Start
Safety
- Genetic safety - ask for "Excerpt/wrapper of Formblatt Z" for each new project - to describe GMOs, send to CAi
- Chemical safety - corrosion, toxic substances
- Laser safety - no mirrors, opening boxes, etc. - and complete the laser safety course!
- Log-book writing and error reporting, how to do.
Booking
- Booking policies (show website: 3 h slots, 4-wk in advance max)
- Don't book and then just before, remove a massive session
- We use the booking system to generate bills
Incubator
- We keep it at 21.5°C, all the time (do not leave it open!)
- Other cooling: right-side of the table is at 17°C, all the time, for the objective turret
- Leave coolings on!
Switch-on
- Buttons in numbered sequence
- Pause between buttons, do you need the fluorescent lamp?
Log-in
- TCS user - machine - DMI8 stage
- Generally non-active (but optionally on):
- Resonant scanner (greatly increase scan speed), STED (high resolution), AFC (adaptive focus control - good for keeping time course in focus)
- Initialize table (for multiple locations imaging; raise microscope arm first, objectives go down automatically)
Software - lasers
- Laser config: STED vs. non-STED
- Which lasers do we have? What do they do? WLL (pulsed, pick wavelength, gating), Argon (more powerful, fan cooling)
- How to switch them off (especially Argon)
- The fluorescent lamp needs at least 30 minutes between off-on
Touch panel
Table inlet
- Is for fine z-adjustments, eg. active when xz-scanning
- Do not lean on, or push down hard on!
Sample placement/preparation
- Table sample holder: move holders to accomodate sample - leave open to allow raising sample
- Objective selection + apply immersion oil
- Focus finding: see droplet become wider, use fluorescence/DIC
Software - overview
- Left: acquisition settings, pixel size, speed etc.
- Middle: beam path, filter settings, detectors etc.
- Right: images already taken, current scan displayed
Beam path
- Go through beam path on-screen, what it schematically represents
- Lasers: switch on check boxes, switch between classic/spectrum-picker views. Start with 2-5% power
- Notch filters: picking laser lines at notch filter wavelengths is preferable over exactly matching the dye's excitation spectrum.
- Detectors: PMT (robust, noisy) vs. HyD (sensitive, advanced functions: gating, photon counting, low noise)
Laser/filter settings
- Picking emission spectrum: Keep laser out of range, at least 10 nm
- Transmitted light on: in parallel to laser scanning -can just activate in any sequential scan
- Show dye spectrum and "dye assistant" (help with setting up scans)
Acquisition
- Rotary knobs on touch-pad, configurable too!
- Autofocus can find focus automatically, but isn't used often (by "hand", rather)
- Live mode (quick and dirty), doesn't take into account detailed settings
Live
- We see nothing at first - why? PMT used, needs gain (600-800), adjust contrast in histogram to keep up
- Motor correction collar: What does it do and why?
- Motor correction can set up on control panel, and can adjust until the signal is brightest (eg. use XZ scanning)
- Use "range indicator" to view live, and to optimize motorized correction - in steps, judge when signal is going down again
Fine tuning acquisition
- Pixel size is important - talk about the extremes, and what's wrong with those
- Optimally, pixel size should be 3-4 times smaller than the expected resolution (which is roughly 1/2 the emission wavelength)
- Pinhole: can change values to increase fluorescent signal intensity, at the cost of resolution
- Averaging is employed (not in live) to counteract noise, such as PMT detector noise
- Accumulation is employed (also in live) in situations with low signal intensity, but also low noise
- Optimise the signal for each channel using laser intensity, detector gain, scanning speed, averaging/accumulation, zoom, and display range
- Optional: smooth rendering (leica display option) can be disabled, r/clicking the channel image
Multi-channel experiments
- Activate T-PMT → immediately have a multi-channel experiment
- Mention sequential scanning (line, frame)
- Add channel ("Seq")
- Cannot change detector order, physically arranged that way
- Add a laser line + detector window, point out you need to switch them on/off in each sequential scan
- Dye Assistant does these things automatically, but needs scrutiny
- Can use Dye Assistant to point out potential cross-talk and bleedthrough issues (spectra are visualised)
- The real way to address bleedthrough/crosstalk problems: USE CONTROL SAMPLES! With eg. only one colour of fluorophore expressed.
- Then, suspicious signal can be evaluated; does it occur in the sample itself? or because of the other fluorophore? at all?
Z-stacks
- Use gentle imaging conditions, and the control-panel Z-controls, define top and bottom of the stack
- The knobs on the microscope control the height of the whole table, the knob on the control panel controls the smaller Z-inlet
- Change step-size, best is system optimized, but can reduce them a bit
Time series/focus control
- Define total experiment time, and intervals between acquisitions
- The series will use the currently active acquisition settings (speed, format, etc.)
- Now the Automated Focus Control (AFC) becomes relevant, which uses IR laser reflection to hold-current-position over time
- "Show autofocus channel" can show what's going on there
HyVolution
- PSF always messes up your image, but can be partially countered using deconvolution
- HyVolution slider drags between best speed and best resolution, for deconvolution
- Enter which mounting medium was used
- Change from aggressive-standard-weak setting; test same acquisition region for the differences
- Try to overdo it, get artifacts, to show what it looks like when going wrong
Saving
- Can save data locally during the experiment,
- Then transfer to the web drive (Daten) at the end of the session
- We do not take responsibility for data locally saved!
- Can make "collections" out of images to create separate LIF files
- Keep LIF files, use FIJI to analyze them, export things from there
Switch-off
- Depends on next user: if same-day, can keep system on
- Clean the objectives with a few wipes using a Kimtech-wipe
- Lasers off in software, wait for Argon laser to cool (can hear)
- Then, switch off PC, and reverse-order the power buttons on the panel
- Close the incubator and write session details in log-book