Overview

CellView is a local DuckDB-backed database that sits between the OMERO-Screen analysis pipeline and your downstream data analysis. It stores single-cell measurements from high-content immunofluorescence screens in a structured, queryable form so you can browse, filter, and export your data without touching the OMERO server again.

Workflow overview

OMERO-Screen
(per-plate CSV results)
      |
      v
   [ import ]
cellview import csv / plate / screen
      |
      v
  [ explore ]
cellview projects / experiment / plate
      |
      v
 [ Python API ]
cellview_load_data(plate_id, ...)
      |
      v
   [ plots ]
omero-screen-plots / your own notebooks

Key capabilities

  • Import single-cell measurements from CSV files, individual OMERO plates, or entire OMERO screens into a structured DuckDB database.
  • Browse projects, experiments, plates, and conditions via a rich terminal interface.
  • Edit project and experiment metadata interactively.
  • Delete plate records and all associated measurements safely.
  • Export plate data as pandas or polars DataFrames for analysis.
  • Explore data interactively by launching a pre-populated Jupyter notebook from customisable templates, with an optional Napari viewer.
  • Templates — ship your own analysis notebooks and launch them with a single command.
  • Python API — load data directly into DataFrames from scripts or notebooks with a single function call.