What it does
CellProfiler processes biological images through a sequence of image-processing modules and exports measurements to a spreadsheet or database.
Load an example pipeline, adapt the image/module settings and choose outputs before processing. Measurement and image exports are separate. The 4.2.8 manual's ExportToSpreadsheet writes delimited text; ExportToDatabase provides database-oriented output such as SQLite or MySQL. Processed images are not saved automatically: add SaveImages when those files are needed. Metadata can organize measurement subfolders, but Experiment.csv stays in the default output folder under that version's rule. Keep the pipeline and settings with the intended measurements and image outputs.
Strengths
- Modular processing pipelines
- Spreadsheet and database output
Best for
- Repeating an image-analysis method across a set
Sources
- CellProfiler (Oct 26, 2026)
- CellProfiler measurement and image output modules (Oct 26, 2026)