Arbitrary Line Scan Tab (Galvo)

Line scans are used to acquire data from a sample at very high frame rates. Instead of the raster scan pattern that is applied in the 2D Frame mode the user can define a custom trajectory for the mirrors to scan and data will only be collected from the pixels that the trajectory passes through creating an intensity profile of those pixels over time. The speed of acquisition will depend on the complexity of the specified path.

Setting Trajectory

Line Scan trajectory before and after confirmation. Red circle and line indicate start and direction.
Line Scan trajectory before and after confirmation. Red circle and line indicate start and direction.

The arbitrary line scan function is selected by clicking the arbitrary line scan tab.. The line scan tool will generate a trajectory for the scanning mirrors to follow based on a user drawn line.

  • Select the tab and click Channel to select which channel you would like to record from.
  • Click Focus to bring up a live image of the sample.
  • Find the area you would like to execute the line scan through.
  • When happy with the FOV click Focus or Cancel to freeze the image.
  • Use the freehand or polygon line tool to draw a closed path through the structures you would like to record from.
  • When complete, press Confirm Line.

Once confirmed, a red circle will appear around the start/end point and part of the line will be turned red to indicate the direction of the scan. The mirrors will scan in the direction you have drawn the line.

When confirmed, snapshot of your current FOV with the drawn line is taken and saved with a date and time stamped name in the root folder alongside a CSV coordinate file for the drawn line.

Loading Coordinates

The Load Coordinates system allows users to load in a CSV-text file of pixel coordinates and automatically prepares a trajectory between them.

As mentioned above a CSV-text file is generated with each line scan and can be re-used by loading the file.

To generate your own CSV-text file for use with the load coordinate system first take a reference image using SciScan.

Load the image into your chosen image analysis program and identify the pixels you would like the line scan to pass through.

Save these values as an ASCII text file with comma-separated values.

Focus on the same position in SciScan (use the Position Save Module) to ensure you are lined up exactly as before.

Click Load.Coordinates and navigate to your saved .csv file, this should automatically draw a line through the pixel coordinates in the saved in the file.

Please note that some analysis packages (i.e. Matlab) will begin counting at 1 while SciScan begins counting at 0, this may result in a 1px shift that needs to be corrected for beforehand. Other analysis programs might count pixels in a different way which could result in an X or Y inverted trajectory.

Setting Scan Parameters

Once a line is confirmed it will activate the 2D line tab. This tab allows you to change the number of frames to acquire and lines to display in the channel pane as well as giving you information about the number of pixels in your line and the speed at which it will scan the path.

2D Line Scan Tab

 

 

 

 

 

 

 

 

 

LabelNameFunction
Ano. of lines to acquireThe number of lines you wish to save when record is pressed
BLines to display at onceThe number of lines to display per "frame" in the image display window.
Cpixels per lineDisplays how many pixels are in the confirmed trajectory.
Dlines per secondMaximum speed the chosen path can be scanned at.

Viewing or Recording Line Scans

You can view a preview of your line scan by pressing Focus or can move straight to recording from the sample by pressing Record. Line Scan data will be saved and visualised as below, each line represents one pass around the confirmed trajectory meaning that any changes in intensity will be seen between each line.

Resulting image from trajectory above. Bright lines indicate the structures the path passes through.
Resulting image from trajectory above. Bright lines indicate the structures the path passes through.

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