CloudScope is an image loading, visualization, and analysis application.

It provides desktop and browser interfaces for working with acquisition-backed image data. The desktop and web GUIs use the exact same interface. Current quantitative analysis workflows are designed for line scan kymographs and include:

• in vivo blood flow velocity analysis using a Radon-transform-based method
• vessel diameter analysis
• peak detection for functional fluorescence reporters (like GCaMP)

For folder-level comparison of analysis results across many files, CloudScope provides pool plots — interactive velocity and peak summaries that update as you load data and run analyses. See the Pool plots guide.

• Launch the web app

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  Try CloudScope in your browser before installing a desktop build.

  Open cloudscope.mapmanager.net

• Get the desktop app

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  CloudScope desktop is the same application on macOS and Windows. Request a build, then follow the platform install steps in the documentation.

  Get the desktop app

Why CloudScope?

CloudScope separates data handling from user interfaces so workflows stay reproducible across desktop, browser, and scripting.

CloudScope is built on two open-source packages:

• AcqStore — acquisition-backed file loading, ROIs, metadata, and scientific analysis
• NiceWidgets — reusable NiceGUI widgets used by the CloudScope interface

Use cases

CloudScope ships the same interface as a desktop app and a web app. Both use the AcqStore backend, which also supports scripting. That shared stack enables workflows that are uncommon in scientific analysis software:

On the scope
Run the desktop app on your acquisition or ePhys setup to visualize and analyze data while it is being collected.

Offline analysis
Use the same GUIs and AcqStore scripting for lab analysis. The web app makes it easy to share work with collaborators in the lab or remotely.

When you publish
Serve CloudScope as a web app with your dataset so readers get the same interface you used on the scope and in the lab — to inspect results, and to extend the analysis.

One backend, multiple interfaces

The GUI is a front end for shared scientific analysis code in AcqStore. Measurements run in the app can be reproduced and extended from Python in AcqStore notebooks and APIs without reimplementing the algorithm.

Supported file formats

CloudScope supports these commercial microscopy formats:

• Olympus / Evident .oir
• Zeiss .czi
• Nikon .nd2

and these open image formats:

• TIFF .tif
• OME-Zarr .ome.zarr

See Supported file formats for format-specific notes.

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.

Next steps

• Using the GUI — interface overview, loading and saving, and sample data
• Recipes — step-by-step analysis workflows

Algorithm parameters, notebooks, and programmatic APIs are documented in AcqStore.