@@ -165,6 +165,8 @@ Always tick 'Save Sequence to Disk' and set a path under 'Directory' (ideally sa
### 3. Set up your experiment/sequence
Set up your experiment and then press 'Sequence':
#### Time-lapse
Tick Time-lapse and choose your number of time points, your time interval or your duration. You only have to choose two of them and the third one will adapt automatically. If you are only doing a time-lapse (no other wavelengths, z-series or stage positions), you can also tick 'streaming' for a faster recording. The time interval is only the waiting time between two time points, after which an image is recorded and needs to be read out from the camera chip (so there will always be a couple of 10-100ms added to your time interval, which you can read out from your metadata). If you set a time interval of 0 the recording will be done as fast as possible (meaning the time interval is then only the Exposure time plus the readout time of the camera - multiplied by the number of wavelengths, z-planes and positions, depending on your experiment: also switching in between wavelengths or moving to different z-planes or positions takes time!). If you set a time interval >0 then it will automatically be increased, in case you have chosen it too short for your number of wavelengths, z-planes and/or positions. If you still want to further decrease your time interval, you have to reduce your number of wavelengths, z-planes and/or positions per time point.
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@@ -205,7 +207,7 @@ a. Tick 'Stage positions' and then choose 'Scan slide' in the dropdown menu.
b. Choose the Fill Order 'Vertical' and click on the square symbol right below (it only shows when you hover over it with your mouse) - the Scan Slide Detail View should open
c. Click on 'Setup' in the right upper corner, then close just the Scan Slide Detail View
c. Click on 'Setup' in the right upper corner, choose the right objective and overlap, then close just the Scan Slide Detail View
@@ -223,8 +225,17 @@ g. Open again the Scan Slide Detail View.
h. Click 'clear'. Then go to 'Show Live' and use the joystick/controller to move around your sample and define the area you want to scan. If you have moved to far, go to the side that you want to reduce (corners do not work), click inside the Scan Slide Detail View window & press Control + Shift while moving the joystick to reduce the area.
i. Record an overview image.
i. Choose a desired overlap between tiles
j. Record an overview image
k. Drag a rectangular ROI around the structure you want to record in your overview image
l. You can set focus points by going to 'show live', double clicking in your overview image and changing the focus
m. Record your sequence and process it in VisiView our Imaris
