Saved file formats¶

When you save work in CloudScope, files are written next to the source image file on disk. The original image file is never modified.

For a source file named my_file.tif, CloudScope may create:

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

Which files appear depends on what you have loaded, edited, and analyzed. CloudScope reloads saved files automatically the next time you open the source image.

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

JSON file (`my_file.tif.json`)¶

The JSON file stores CloudScope state for one acquisition file. It includes:

Content	Description
Accepted / rejected state	Whether the file is marked accepted in the file list
Experimental metadata	User-editable experiment fields (species, condition, notes, and related fields)
Image header metadata	Header fields read from the file, including physical unit and axis label calibration
ROIs	Line and rectangular regions of interest
Analysis records	One entry per analysis (velocity, diameter, peak detection, velocity events, and others) with detection parameters and summary values
Image contrast	Per-channel display contrast settings (when present)

Analyses that produce large tabular output store summaries and parameters in the JSON file. Row-by-row tables are stored in CSV files when an analysis provides CSV export.

Analyses stored primarily in JSON¶

Some analyses do not write a separate CSV file:

Analysis	JSON contents
Velocity events	Event definitions, event parameters, and event summary statistics (managed in the Velocity panel)
Heart rate	Summary values derived from a velocity time series (notebook workflow today; no dedicated GUI panel)

See Velocity event analysis for the GUI workflow.

CSV files (tabular analysis output)¶

When an analysis produces a results table, CloudScope saves a CSV file named <source-file>.<analysis-name>.csv.

Analysis	CSV filename	Typical contents
Velocity (Radon)	`my_file.tif.radon_velocity.csv`	Per-window velocity measurements and related columns
Diameter	`my_file.tif.diameter.csv`	Per-line or per-profile diameter measurements
Sum intensity (peak detect)	`my_file.tif.sum_intensity.csv`	Detected peak events and related trace columns

CSV files are suitable for export to spreadsheets or downstream Python analysis.

Save actions in the GUI¶

From the load/save controls:

Save Selected — saves the currently selected file when it has unsaved changes (metadata, ROIs, contrast, or analysis edits). Disabled when nothing is selected or the selection has no pending changes.
Save All — saves every loaded file that has unsaved changes.

Both actions write the JSON file and any analysis CSV files that need updating for the affected acquisition files.

Export TIFF¶

CloudScope can also export TIFF files. These are separate from the JSON/CSV sidecars written by Save Selected / Save All. Exports create a new TIFF; they do not modify the source acquisition file.

Action	Where	What is written
Save As Tif...	File list context menu	Primary acquisition pixels for the selected file as a TIFF (native save dialog on desktop; browser download in the web app).
Save Reference As Tif	Reference Image panel	Full multichannel reference/overview image as a TIFF when a reference is present. Suggested name is `<source-stem>-reference.tif`. ImageJ X/Y resolution is written from the reference spatial calibration when available. Scan paths and line ROIs are not burned into the exported pixels.