GraphCompass: spatial metrics for differential analyses of cell organization across conditions. - Mayar Ali; Merel Kuijs; Soroor Hediyeh-Zadeh; Tim Treis; Karin Hrovatin; Giovanni Palla; Anna C. Schaar; Fabian J. Theis (Bioinform., 2024)

cp_measure: API-first feature extraction for image-based profiling workflows. - Alán F. Muñoz; Tim Treis; Alexandr A. Kalinin; Shatavisha Dasgupta; Fabian J. Theis; Anne E. Carpenter; Shantanu Singh (CoRR, 2025)