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Sum intensity analysis

Sum intensity analysis measures normalized line intensity along a line scan kymograph ROI and detects transient peaks from a functional reporter (like GCaMP). The analysis computes delta-F over F0 (df/f0), applies derivative-threshold onset detection by default, and refines peak locations in a search window around each onset.

Before you start

  • Load a line scan kymograph (.oir, .czi, .tif, or .ome.zarr).
  • Select or create a rectangular ROI covering the region to analyze.

See Using the GUI for loading files and ROIs.

Run sum intensity analysis in the GUI

  1. Select the file, channel, and ROI in the file list.
  2. Open the left navigation toolbar and click Peak Detect (functions icon).
  3. Choose a Detection preset (fast, medium, or slow) or tune individual detection parameters.
  4. Click Run Sum Intensity Analysis.
  5. Review the plot: df/f0 trace, derivative, onset markers, and peak markers.
  6. Use Save Selected or Save All in the top header to persist results.

CloudScope sum intensity analysis view

Optional plot overlays (context menu on the sum-intensity plot):

  • Show or hide the derivative trace on the secondary y-axis.
  • Show or hide a diameter trace when diameter analysis has been run on the same file, channel, and ROI (default off).

Results and reproducibility

Review sum-intensity results in the Peak Detect panel and the Sum intensity plot at the bottom of the Home page. Save from the top header to write JSON and CSV files next to the source image.

The GUI and scripting workflows share the same acqstore backend, so results from the interface should match equivalent Python scripts using the same data, ROIs, and parameters. See Saved file formats for output file details.

Saved files

For a source file named my_file.tif:

my_file.tif.json
my_file.tif.sum_intensity.csv

The JSON file stores detection parameters, summary values (for example peak count and F0 baseline), and event records. The CSV stores per-timepoint tabular traces and onset/peak markers.

See also