Region of Interest (ROI) Monitoring (Resonant)

SciScan’s ROI monitoring feature allows you to draw a region of interest and plots a graph of the mean grey value of the pixels within that region over time. Multiple ROIs can be selected and monitored simultaneously. This can give a good indication of how fluorescence changes over time eg. In response to electrical or sensory stimulation; particularly useful for calcium imaging.

ROI Monitor Tab (Resonant)
ROI Monitor Tab (Resonant)

Please note: This feature is intended only for online guidance during the experiment and should not replace a detailed offline analysis of the recorded images.

Please note: At very high frame rates SciScan prioritises saving and displaying data and the module may not be capable of calculating the mean pixel intensity fast enough. Data points on the graph will be dropped from the graph.


Select the ROI monitoring feature by click on the ROI tab in the channels bar

  • Click on channel (right hand side of display window) to select which PMT you would like to monitor then click Focus to bring up a live image
  • Select any of the available tools (freehand, polygon, ellipse ect…) to add a ROI to the image. All ROIs must be closed loops, SciScan will not measure pixel intensities over time for a line
  • Hold the CTRL key to add additional ROIs
  • Clicking anywhere on the image without CTRL pressed will remove all active ROIs
  • The graph at the bottom of the pane will update automatically with the mean grey values for the pixels within each ROI, assigning a different colour to each for easy recognition.
  • Right click on the graph to export as a simple image or .csv file

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