Tutorials and Examples
The following notebooks walk through key SCALLOPS workflows, from getting familiar with the library’s data model to running a complete end-to-end Optical Pooled Screen (OPS) analysis. They are designed to be followed in order for new users, though each notebook can also be consulted independently as a reference.
All notebooks can be run locally with a working SCALLOPS installation (see Installation). Example data paths in the notebooks may need to be updated to reflect your local setup.
End-to-End Tutorial
A production-grade walkthrough of the full SCALLOPS pipeline using the PERISCOPE dataset. Covers every major stage in sequence: illumination correction, image stitching, ISS registration, cellular segmentation, spot detection, base calling, feature extraction, and final data merging. This is the recommended starting point for understanding how all components fit together in a real experiment. Downstream analyses, quality control, and visualization are explored in more depth in the OPS Analysis and Plotting notebooks.
OPS Analysis
A focused walkthrough of the Optical Pooled Screening analysis steps: ISS image registration, nuclei and cell segmentation, spot detection and base calling, barcode assignment to cells, and phenotypic feature extraction. Includes visualization and quality-control metrics throughout. Useful as a reference for any individual OPS analysis step.
Plotting
A showcase of SCALLOPS’ built-in visualization tools. Covers composite image plotting, cross-talk analysis, distribution plots, heatmaps, histograms, and image display utilities. Also demonstrates Napari-based interactive exploration for OPS data. Useful as a quick reference when building figures or inspecting results.
Data Structures
An introduction to SCALLOPS’ core data model. Demonstrates how to read individual images and full experiments, concatenate image collections across dimensions, apply functions across an experiment, and save and reload data using the Zarr format. Useful for understanding how SCALLOPS represents and manipulates imaging data.
Barrel Distortion Estimation
A tutorial on identifying and correcting optical barrel distortion in microscopy images. Explains the mathematical model behind barrel distortion and walks through the interactive workflow in Napari for estimating and applying the correction coefficient. Relevant for users working with wide-field objectives or lenses that introduce radial distortion.