{"doi":"10.3390/biom15091237","title":"Depth Correction of TOF-SIMS Depth Profiling Images Using the Total Ion Count Images","abstract":"Depth profiling time of flight secondary ion mass spectrometry (TOF-SIMS) enables imaging the distributions of unlabeled metabolites within cells. When depth profiling TOF-SIMS is performed on intact cells, the 3D renderings produced by stacking and rending the individual depth profiling images are distorted along the z-axis, which complicates image interpretation. Here we describe an approach for correcting the z-axis distortion in 3D TOF-SIMS depth profiling images of cells. This approach uses the total ion images collected during TOF-SIMS depth profiling to create a 3D morphology model of the cell's surface at the time when each depth profiling image was acquired. These morphology models are used to correct the z-position and height of each voxel in the component-specific 3D TOF-SIMS images. We have applied this approach to 3D TOF-SIMS depth profiling images that show endoplasmic reticulum-plasma membrane (ER-PM) junctions in cells that are a simplified model of ER-PM junctions in neuronal cells. The depth corrected 3D image more accurately depicted the structure of the ER-PM junctions than the uncorrected image. Projection of the depth corrected 3D image on the model of the cell's morphology facilitated visualization of the ER-PM junctions relative to the peaks, ridges and valleys on the surface of the cell. Thus, accurate component-specific 3D images may now be produced for depth profiling TOF-SIMS datasets. This approach may facilitate efforts to identify the lipids and other metabolites that reside in ER-PM junctions in neuronal cells and elucidate their roles in neuronal function.","journal":"Biomolecules","year":2025,"id":573499,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9561,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":527427,"name":"Brittney Gorman","orcid":"0000-0002-5087-3606","position":1,"is_corresponding":false},{"id":527429,"name":"Mary L. Kraft","orcid":"0000-0002-5879-7222","position":2,"is_corresponding":false},{"id":527428,"name":"Melanie A. Brunet","orcid":"0000-0002-8812-5216","position":0,"is_corresponding":true}],"reference_count":41,"raw_metadata":null,"created_at":"2026-07-19T02:57:32.445190Z","pmid":"41008544","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}