Hardware problems

There is no image

You might sometimes encounter the situation where you have finished trimming, moved the sample in XY under the objective but there is no signal. Now what? The following is a series of checks you can make. Follow them in order. Don't waste time restarting BakingTray and ScanImage as this is almost never going to help.

1. Is the laser shutter open? See indicate on GUI.

2. Is the laser modelocked ("pulsing"). See indicator on GUI.

3. Is the laser power set to a value to typically use? Is the laser wavelength correct?

4. Are the lights in the enclosure turned off?

5. Are the PMTs turned on in ScanImage? Are the PMT gains reasonable?

6. Is the PMT power supply (external controller box) turned on?

7. Did you check the GUI boxes to display at least one channel in ScanImage?

8. Right click on the channel image window and confirm the look up table is set appropriately given the image histogram.

9. If you have a Pockels cell, is it switched on?

If everything above checks out then everything is set up as expected and something else is wrong. Likely either there is no sample visible under the objective, or the laser is not reaching the sample, or the emitted signal is somehow not being detected. Let's deal with these one at a time.

Check the excitation path

Set the laser to a visible wavelenth, such as 790 nm, and scan at about 150 mW. Turn off the PMT power supply box (leave on the PMTs in ScanImage) and confirm that you see the beam coming out of the objective and scanning over sample. If the beam is over the agar, move the sample in X/Y until it is being scanned try obtaining an image again.

The beam is very bright so even if it looks like it is scanning over the sample, it is possible that most of the beam is being occluded somewhere. If possible, whilst scanning, place a white card in the space between the objective and the lens behind it. You should see a red blurry disk. If it is a weird shape then something is in the excitation path.

If you have been laser safety trained and feel confident, you can follow the beam back along the path with a piece of card and confirm whether something is occluding it.

Laser connection fails

BakingTray controls the laser so that acquisition can be automatically halted if the laser stops pulsing (modelocking). The laser can be controlled via the the "Laser" button in the main GUI.

Sometimes initial connection to the laser fails. If this happens try the following. Firstly, attempt to open the laser shutter because sometimes the laser is in fact connected: hBT.laser.openShutter If that fails (it returns 0) then you will need to try disconnecting and reconnecting to the laser with hBT.renewLaserConnection. You can also try this manually:

delete(hBT.laser)
hBT.laser = maitai('COM1'); % assuming you have a MaiTai on COM1
hBT.laser.parent = hBT;