Outputs

Save geometry and measurements at different stages to inspect an analysis or resume it without repeating every step.

Common outputs

Output	Contents	How it is produced
masks/*_cp_masks.tif	Integer segmentation labels for each selected field.	segment_images() via Omnipose.
<dataset>_meshdata.pkl	Cell IDs, field metadata, contours, midlines, and meshes.	batch_process_mesh(save_data=True).
<dataset>_curated_meshdata.pkl	Geometry for cells retained by curation.	curate_dataset(save_curated_data=True).
<dataset>_meshdata.parquet	Reloadable geometry stored as nested numeric lists.	meshdata_to_parquet().
<dataset>_features.pkl / .parquet	Merged per-cell feature table.	dataframe_to_pkl() / dataframe_to_parquet().
curated_masks/*.tif and curated_mask_provenance.csv	Rasterized retained contours and original-label overlap records.	export_curated_masks().

The default dataset name is the final component of image_folder_path. Renaming a working-copy folder therefore changes default output names. Use explicit filenames when that matters.

Identity columns

The ordinary table uses image_name, cell_id, and frame. A cell ID is local to a field; use all identity columns when joining tables. frame is the image’s collection index and is not evidence of temporal tracking. include_metadata_tag=True renames these columns to Metadata_image_name, Metadata_cell_id, and Metadata_frame.

See Merge tables and save results for naming, serialization, overwrite behavior, and how to preserve processing summaries alongside measurements.