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Velocity analysis

Velocity analysis estimates in vivo blood flow velocity from line scan kymographs using a Radon-transform-based method.

Before you start

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

See Using the GUI for loading files and ROIs.

Run velocity analysis in the GUI

  1. Select the file, channel, and ROI in the file list.
  2. Open the left navigation toolbar and click Velocity (speed icon).
  3. Review Detection parameters in the Velocity panel.
  4. Click Run Radon Analysis.
  5. Review the results summary and plotted output.
  6. Use Save Selected or Save All in the top header to keep results.

CloudScope velocity analysis panel

Optional: click Batch analysis to preview or run velocity analysis across multiple loaded files with shared ROI settings.

Results and reproducibility

Review velocity results in the Velocity panel, the Analysis plot, and the primary image viewer. 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.radon_velocity.csv

The JSON file stores detection parameters and summary values. The CSV stores per-window tabular velocity results.

Next steps