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cytominer-database provides command-line tools for organizing measurements extracted from images.

Software tools such as CellProfiler can extract hundreds of measurements from millions of cells in a typical high-throughput imaging experiment. The measurements are stored across thousands of CSV files.

cytominer-database helps you organize these data into a single database backend, such as SQLite.

Why cytominer-database?

While tools like CellProfiler can store measurements directly in databases, it is usually infeasible to create a centralized database in which to store these measurements. A more scalable approach is to create a set of CSVs per “batch” of images, and then later merge these CSVs.

cytominer-database ingest reads these CSVs, checks for errors, then ingests them into a database backend, including SQLite, MySQL, PostgresSQL, and several other backends supported by odo.

cytominer-database ingest source_directory sqlite:///backend.sqlite -c ingest_config.ini

will ingest the CSV files nested under source_directory into a SQLite backend

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