Spatial µProBe: a correlative multimodal imaging approach for spatial profiling of biological micro-environments

Description: This resource contains the datasets and supporting materials for the publication "Spatial µProBe: a correlative multimodal imaging approach for spatial profiling of biological micro-environments". The files are structured in the following categories: "data" (datasets from raw data to processed outputs generated in the study), "demo" (data and videos highlighting how to use the tool) and "code" (copy of the main tool at the time of submission and supporting scripts to generate figures and results). Data: For each zip file, the contents are ordered based on the step of the analysis at which the files were generated (0: raw data, n-1: intermediate analysis, n: processed outputs), and the folder names include a short descriptive keyword of each step. data_BoneSegmentation.zip - files related to the analysis of bone histological sections using deep-learning models. Includes segmentation results from Optuna optimization and model predictions. data_LivEMechanoregulation.zip - files related to the analysis of Local in vivo mechanical Environments and mechanoregulation analysis of the mouse femur and caudal vertebra models, using spatial transcriptomics data. Includes data from the mouse femur (BCR Control and Loaded) conditions and caudal vertebra (WT vertebra), with outputs including histological 2D data, micro-CT analysis, 2D-3D registration output, SCTransform of ST data, SPARK-X spatial analysis, Starfysh analysis and GAM/iStar-SPARKX statistical modeling results. data_LivEProfiling.zip - files related to the analysis of Local in vivo mechanical Environments based on histological sections of the mouse femur. Contains a dataset of histological sections, micro-CT images and the outputs of micro-finite element analysis. data_Validation_InSilico.zip - files related to the in silico validation of the 2D-3D registration algorithm. Contains the outputs of the unimodal study to assess the convergence of the 2D-3D registration algorithm, the preliminary comparison of image similarity functions and the reproducibility analysis. data_Validation_Landmarking.zip - files related to the validation of the 2D-3D registration algorithm using manual landmarking. Contains the ex vivo high resolution and in vivo micro-CT scans and the corresponding histological sections for the mouse caudal vertebra samples, the output of the Slicer3D landmarking analysis and the output from Spatial µProBe, as well as the analysis of histological deformations based on the landmarking positions. Demo: demo_data.zip - example dataset to try the pipeline. demo_tutorial.zip - a collection of short videos with an example of the complete pipeline using the demo data. Code: code_spatial-microprobe-main.zip - a clone of the GitLab repository with the release version 1.0.0 (created on 2025-06-26). code_supporting_scripts.zip - a collection of scripts used to generate all the results and figures.