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End User Guide

CloudScope lets you load raw image files, visualize image data, define and select ROIs, run supported analyses, and export results.

Current quantitative analysis workflows are designed for line scan kymographs and include:

Try CloudScope in a browser

The fastest way to try CloudScope is the public browser application:

Open the CloudScope Web Application

The browser app provides the same GUI and analysis workflows as the desktop app.

Get the desktop app

CloudScope desktop is the same application on macOS and Windows. Start with Get the desktop app — request a build via the form, then follow the Windows or macOS install steps after you receive the ZIP.

Supported file formats

CloudScope supports commercial microscopy formats — Olympus / Evident .oir, Zeiss .czi, and Nikon .nd2 — and open image formats — TIFF .tif and OME-Zarr .ome.zarr.

See Supported file formats for format-specific notes.

Support for commercial microscopy formats builds on the Python imaging ecosystem. CloudScope gratefully acknowledges Christoph Gohlke for long-standing work on microscopy and file-format tooling.

Sample data

CloudScope integrates with the cloudscope-data Repository. From the history menu () in the load/save controls, choose:

  • Load Velocity Sample Data — OIR kymograph data for velocity analysis
  • Load Diameter Sample Data — TIFF kymograph data for diameter analysis

CloudScope downloads and caches the sample folder automatically. Sample data is useful for learning the interface, testing analysis workflows, and confirming that a new installation is working.

See Using the GUI for screenshots and menu details.

Basic workflow

A typical CloudScope workflow is:

  1. Open CloudScope in the browser or launch the desktop app.
  2. Load sample data from the history menu, or open local image files.
  3. Select an image file in the file list.
  4. Visualize the image and choose or create an ROI.
  5. Run a supported analysis.
  6. Review results in the GUI.
  7. Save or export results.

See Using the GUI for a visual guide to the main interface.

For comparing analysis results across a loaded folder, see Pool plots.

Saved files

CloudScope saves analysis state and tabular results next to the source image file. For a source file named my_file.tif, saved files may include:

my_file.tif
my_file.tif.json
my_file.tif.radon_velocity.csv
my_file.tif.diameter.csv
my_file.tif.sum_intensity.csv

The JSON file stores metadata, ROIs, analysis parameters, and analysis summaries. CSV files store tabular outputs for analyses that provide CSV export.

Do not delete the .json or .csv files if you want CloudScope to reload prior ROIs, parameters, and results.

See Saved file formats for a complete description of JSON and CSV contents, including velocity events and each analysis type.

Current limitations

CloudScope is a general image loading and visualization application, but the current quantitative analysis workflows are focused on line scan kymographs.

Traditional two-dimensional image analysis workflows are not yet implemented as dedicated CloudScope analysis modules.

Where to go next