The two csv files summarize refinements applied to COSEM predictions to produce the final segmentations described in the paper. organelle_refinements contains refinements for the organelles themselves, whereas contact_refinements describes the refinements applied for contact site analysis. These refinements are also provided in a google doc, which also contains a summary of some of the analysis results.
Note: A unique refinement is used for the peripheral ER. The peripheral ER is calculated as the refined ER masked with an expanded version of the refined nucleus. The nucleus expansions are 80 nm, 80 nm, 150 nm and 200 nm for jrc_hela-2, jrc_hela-3, jrc_jurkat-1 and jrc_macrophage-2, respectively. The reconstructed ER (as described in the paper) is also masked in this way. Thus, two peripheral ERs exist. When discussing and reporting morphology based ER measurements, or contact sites between peripheral ER and mitos or ribosomes, we use the peripheral reconstructed ER; otherwise, the original peripheral ER is used. Additional masking as described for contact sites also applies to these peripheral ERs.