Data Analysis Core

PROJECT SUMMARY – Data Analysis Core. The characterization pipelines built by the VU Biomolecular Multimodal Imaging Center (BIOMIC) Data Analysis Core (DAC) will produce a multimodal molecular atlas of kidney across multiple scales in 2-D and 3-D, comprising rich and varied molecular data from MALDI IMS, MxIF, CODEX, spatial and non-spatial proteomics/ transcriptomics, united by common spatial coordinate space. The DAC will build on our previous developments, including spatial segmentation for both acquisition and analysis, comprehensive molecular identification across modalities, automated data mining across modalities by spatial masks using clinical and temporal cues, and situating data within an “average” human kidney developed from 1000s of medical images. In Aim 1 we will further develop and scale our modality-specific processing methods to prepare the different measurement types for subsequent spatial integration, multimodal analysis, and content/cross-omic relationship mining. Aim 2 will focus on expanding and scaling our characterization pipeline, bringing together the broad array of distinct imaging and -omics measurement types individually processed by the methods in Aim 1. By integrating these varied datasets spatially, temporally, as well as content-wise, we will empirically mine them for cross-modal and molecular-functional relationships. These technologies will establish both 2-D and 3-D multimodal tissue maps that concurrently report hundreds to thousands of biomolecules at cellular resolutions, together with corresponding functional and cell type annotations. In Aim 3 we will compose all spatial and molecular information into a reference atlas by expanding the spatio-temporal mapping of molecular variation, organization, and function beyond single tissue block analyses (as in Aim 2) to multi-block and multi-donor tissue cohorts. Finally, Aim 4 will enable continued coordination with the HuBMAP consortium and HIVE team members by integrating our analyses into the HIVE’s ASCT+B tables for interactive exploration, visualization, and searchable analyses.