Where Does CellProfiler Store Data?
CellProfiler saves pipelines as .cpproj files you choose, with prefs in per-OS config. Mirror data paths across machines.
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CellProfiler stores analyses as pipeline files you save by hand. Images stay where your project keeps them. Preferences persist separately in per-OS config locations.
Treat .cpproj files as the portable unit. Config holds UI defaults, not results. Copy pipelines plus data with matching paths, since absolute references break on moves.
Where CellProfiler stores this, by platform
Pipelines wherever saved (.cpproj, prefs in %APPDATA%)
Pipelines as .cpproj files wherever saved. Prefs in per-OS config. Copy pipelines plus images with stable paths.
Pipelines wherever saved (.cpproj, prefs in ~/.config)
Same pipeline files on every OS. Keep data paths identical when moving between machines.
Pipelines wherever saved (.cpproj, prefs in ~/Library)
Same pipeline files. Confirm prefs path in-app across versions.
Frequently asked questions
How do I move a CellProfiler analysis?
Copy your .cpproj pipeline files plus input images to matching paths. Prefs rebuild when missing. Keep module versions aligned between machines.
Pipeline edits disappeared. Why?
Open the pipeline file from wherever you stored it. Pipelines do not auto-save into the app. Save explicitly before closing or edits vanish.
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