[Dataset] ColocZStats: A Z-Stack Signal Colocalization Extension Tool for 3D Slicer

To showcase the capabilities of ColocZStats discussed in its manuscript, we utilized confocal z-stack data collected during a study on the colocalization of DSS1 nuclear bodies with other nuclear body types. DSS1, also known as SEM1, is a gene that encodes a protein crucial for various cellular processes, most notably the function of the 26S proteasome complex in protein degradation. More specifically, a human ovarian clear cell carcinoma cell line (RMG-I) was seeded at 100,000 cells per well onto a coverslip in a 6-well plate and allowed to grow till 70\% confluency. On the day of staining, the cells were fixed with 4\% ice-cold paraformaldehyde for 15 mins at room temperature (RT) and blocked with 2\% Bovine Serum Albumin (BSA) in 0.1\% Phosphate Buffer Saline containing 0.1\% Triton-X (PBSTx) for 30 mins. Following fixation and blocking, the cells were incubated with a primary antibody cocktail containing anti-DSS1 (Catalogue\# NB100-1334, Novus Biologicals) and anti-PML (Catalogue\#sc-966, SCBT) for 1h at RT. After that, the cells were washed 3 times with 0.1\% PBSTx for 5 mins each and incubated with a secondary antibody cocktail containing anti-goat Alexa FluorTM 647 (for DSS1), anti-mouse Alexa FluorTM 488 (for PML) and Hoechst 33342 (Catalogue\# H3570, Invitrogen) for 1h at RT. Following this incubation, the cells were subjected to 3 washes, each lasting 5 mins, with 0.1\% PBSTx to ensure thorough cleansing. Subsequently, z-stack imaging was performed using a Zeiss LSM800 confocal microscope with Airyscan. The above process utilized three distinct dyes to specifically label DSS1 nuclear bodies (Red), promyelocytic leukemia (PML) nuclear bodies (Green), and the nucleus (Blue). The data file was named ‘Sample Image Stack.tif’.