Skip to content

File formats

The cellpy-file format stores the contents of the Data object (frames + metadata) together with a file-version stamp.

Default: v9 .cellpy

In cellpy 2.x, save() writes v9 by default: a zip archive of parquet tables (raw / steps / summary, and optional file-id members) plus typed metadata in meta.json. The usual extension is .cellpy.

c.save("my_run.cellpy")                 # v9 zip-of-parquet
c.load("my_run.cellpy")                 # sniffs v9 vs HDF5

Legacy HDF5

Older v8 (and, with care, earlier) HDF5 layouts remain readable. To write HDF5 explicitly:

c.save("my_run.h5")                     # extension selects HDF5
c.save("out.cellpy", cellpy_file_format="hdf5")

On pip, reading/writing legacy HDF5 needs the optional extra cellpy[legacy-files] (PyTables). Conda packages still ship pytables. Prefer converting once to v9 (cellpy convert old.h5) if you can drop the extra.

Full support matrix and convert recipes: Migrating from cellpy 1.x to 2.x.

Tabular exports

Simple exports to CSV (c.to_csv(out_folder)) or Excel (c.to_excel(out_folder)) are also available.