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Peak detection

Peak detection 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.

In the CloudScope GUI this workflow is labeled Peak Detect on the left toolbar.

Before you start

  • Load a line scan kymograph (.oir, .czi, .nd2, .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 peak detection 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 load/save controls to persist results.

CloudScope peak detection view

Optional plot overlays (context menu on the peak-detection 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).

Edit F0 (baseline)

After a successful peak-detection run, you can adjust the F0 baseline from the peak-detection plot without leaving the Home page:

  1. Right-click the peak-detection plot and choose Edit F0.
  2. An Edit F0 toolbar and F0 plot appear above the df/f0 plot.
  3. Choose one of:
  4. Manual — drag the yellow Manual F0 horizontal line to the desired baseline, then click Set Manual F0.
  5. Percentile (auto) — set the baseline percentile in the toolbar, then click Set Auto F0.
  6. CloudScope re-runs peak detection with the new baseline and updates the plot.
  7. Click Close to leave Edit F0 mode without further changes (or leave after a Set).

Set Manual F0 stores baseline_method="manual" and the chosen manual_f0_baseline. Set Auto F0 stores baseline_method="percentile" and the chosen baseline_percentile. Save with Save Selected or Save All to persist the updated parameters and results.

Results

Review peak-detection results in the Peak Detect panel and the Peak detection plot at the bottom of the Home page. Save from the load/save controls to write JSON and CSV files next to the source image. 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