This dataset contains the complete set of raw experimental data generated for the study on dually detectable nanoparticles used to track encephalitogenic cell fate during induction of adoptive transfer Experimental Autoimmune Encephalomyelitis. It includes physicochemical characterization of nanoparticles, microscopy images, thermographic and MRI-related data, cytometry measurements, in vivo disease scoring, and viability assays. These data enable full reproducibility of the analyses presented in the related publication and allow reuse for nanoparticle tracking, immunological responses, and biomaterials research.

This work was supported by the Spanish Ministry of Science, Innovation and Universities: grants PID2023-149301OB-I00 and PID2021-126325OB-I00 funded by MICIU/AEI (DOI: 10.13039/501100011033) and by ERDF/EU and by Centro de Investigación Biomédica en Red, Instituto de Salud Carlos III. (Refs. CB06/01/0013 and CB06/01/0008). This research work was performed in the framework of the Nanomedicine CSIC HUB (Ref. 202180E048).

**Experimental procedures are fully described in the associated publication (DOI pending).** **Main techniques include:** * Nuclear Magnetic Resonance (NMR) * Thermogravimetric Analysis (TGA) * Cryo-Transmission Electron Microscopy (Cryo-TEM) * Confocal fluorescence microscopy * Flow cytometry * Magnetic Resonance Imaging (MRI) * Thermography * Dynamic Light Scattering (DLS) and Zeta Potential * In vivo EAE scoring

00 - Nuclear Magnetic Resonance 01 - Thermogravimetric analysis 02 - Cryogenic Transmission Electron Microscopy images 03 - MRI (FALTA) 04 - Confocal Imaging 05 - Flow Cytometry data 06 - Alamar Blue data 07 - In vivo data analysis 08 - Thermogram images 09 - Dynamic Light Scattering and Zeta Potential data

All processing, normalization, and analytical pipelines are described at DOI. Raw data is provided without manipulation except for standard export procedures.**

Peer reviewed