{"doi":"10.17504/protocols.io.j8nlkrpmdv5r/v2","title":"Merge multiple 2D MRI datasets as multichannel stacks via ImageJ & Analyze Pancreas Size v2","abstract":"Many MRI datasets are acquired in orthogonal orientations, providing complementary perspectives that are especially useful when segmenting regions of interest. Switching between these views can enhance boundary detection and improve data analysis. However, certain MR pulse sequences—such as T2-weighted scans—are challenging to acquire as full 3D datasets due to pulse sequence limitations or prohibitively long scan times. This is particularly problematic in in vivo imaging, where extended scan durations are not advisable, especially in preclinical studies involving anesthetized subjects with significant disease burden. In this protocol, we outline how we: 1) merge multiple, orthogonal MRI datasets acquired sequentially from the same subject using anatomical fiducial markers. These merged datasets can then be imported into the analysis software of your choice for further processing. 2) segment the pancreas and associated tumors from the stack of merged TIFF images using ImageJ ROI Manager, save and convert these to a mask, and we calculate the volume of the rois using an Excel macro. This approach is especially useful when machine coordinates or MR software cannot overlay datasets, or when such metadata is unavailable. It does, however, require a solid understanding of anatomy and physiology. Our stack merging method serves as an alternative to using licensed software such as VivoQuant, and is particularly valuable in cases where coordinate metadata is inconsistently maintained during data export. We aim to provide a flexible, system-agnostic solution that supports data comparability across different MR platforms and software environments. Some code customization may be necessary depending on how metadata is structured from a particular MR system.","journal":null,"year":2025,"id":568530,"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":0.9173,"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":1473374,"name":"Hoku West-Foyle","orcid":null,"position":1,"is_corresponding":false},{"id":1461817,"name":"Elena Carlson","orcid":null,"position":0,"is_corresponding":true}],"reference_count":0,"raw_metadata":null,"created_at":"2026-07-19T02:56:52.212268Z","pmid":null,"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":[]}