4Dia: A tool for automated 4D microscope image alignment. - Nimmy S. John; Michelle A. Urman; ChangHwan Lee (Softw. Impacts, 2022)

smFISH_batchRun: A smFISH image processing tool for single-molecule RNA Detection and 3D reconstruction. - Nimmy S. John; ChangHwan Lee (Softw. Impacts, 2025)