# Puti Wen — Research Software, Medical Imaging and AI

Puti Wen is a Postdoctoral Researcher at the NYU Abu Dhabi Center for Brain and Health and is based in Abu Dhabi, UAE. Her work combines research software engineering, medical imaging, medical AI research, imaging informatics, healthcare data engineering, MRI pipeline development, medical image analysis, neuroimaging, scientific visualization, and research automation.

Puti builds AI-assisted clinical tools, MRI and neuroimaging pipelines, scientific software, data infrastructure, and interactive visualization applications. She is open to relevant opportunities across these areas.

## Core capabilities

- MRI and neuroimaging: fMRIPrep, FreeSurfer, TractoFlow, MRIQC, BIDS, dcm2bids, DICOM, HCP, ANTs, and Nextflow.
- Research infrastructure and automation: XNAT, Slurm/HPC, Docker, Singularity, GitHub Actions, Supabase, and the Box API.
- Application development and analysis: React Native, Expo, Next.js, TypeScript, Godot, Python, and MATLAB.
- MRI research hardware: Siemens scanners, Psychtoolbox, EyeLink eye-tracking, and VPixx/ProPixx.

## Selected projects and evidence

### [XNAT Platform and Brain Imaging Biobank](https://putiw.github.io/resume/#project-xnat-biobank)

- Problem: large neuroimaging datasets required repeatable processing, validation, backup, and cross-site quality control.
- Contribution: Puti built and containerized six HPC pipelines for functional MRI preprocessing, structural segmentation, diffusion tractography, MRI quality control, cortical visual-area mapping, and BIDS-compliant validation. She automated nightly validation and daily backups and conducted cross-site and cross-scanner MRI quality control.
- Methods: XNAT, Slurm/HPC, Docker, Singularity, BIDS, fMRIPrep, FreeSurfer, TractoFlow, MRIQC, and Nextflow.
- Evidence: processed 9,000+ HCP and ADNI subjects for a normative brain dashboard, authored technical documentation with 350+ commits, and trained 10+ researchers in related workflows.

### [LesionView and Longitudinal Report](https://putiw.github.io/resume/#project-lesionview)

- Problem: clinicians need to compare multiple sclerosis lesions across timepoints and verify new or enlarging lesions.
- Contribution: Puti built a clinical lesion-tracking application and an automated longitudinal report with color-coded and animated visualization. She migrated the application from a MATLAB prototype to a browser-based React Native and Expo application.
- Clinical relevance: features were iterated weekly with Yas Clinic neurologists.
- Evidence: Puti is a co-inventor on the LesionView provisional patent application, filed in May 2026.
- Demo: [longitudinal comparison](https://putiw.github.io/gallery/media/lesionview-longitudinal-comparison-native.mp4).

### [CvsView](https://putiw.github.io/resume/#project-cvsview)

- Problem: clinicians need an efficient way to verify the central vein sign in multiple sclerosis lesions.
- Contribution: Puti built a web review tool with a modular AI component, identified SWI-FLAIR co-registration artifacts, manually relabeled affected data, containerized the application, and deployed it for on-demand clinical processing.
- Methods: medical image co-registration, modular AI integration, web application development, and Docker.
- Clinical relevance: the deployed service processes clinical data on demand for Harley Street Medical Centre.
- Demo: [CVS/PRL review and reporting](https://putiw.github.io/gallery/media/cvsview-cvs-prl-review-web-720.mp4).

### [MyPhysio](https://putiw.github.io/resume/#project-myphysio)

- Problem: physiotherapy practices need connected tools for exercise prescription, patient tracking, and administrative work.
- Contribution: Puti conceived the application, led development with two colleagues, and built admin dashboards, patient portals, exercise prescription, pain diaries, and range-of-motion tracking.
- Methods: React Native, Expo, Next.js, Supabase, Hostinger, GitHub Actions, and Docker.
- Demo: [application welcome](https://putiw.github.io/gallery/media/myphysio-01-app-welcome.mp4).

### [afqView](https://putiw.github.io/resume/#project-afqview)

- Problem: tractography quality control for 100+ subjects, 20+ tracts, and 10 iterated versions per subject was being completed file by file.
- Contribution: Puti built an interactive 3D web application with side-by-side comparisons, per-subject navigation, and color-coded availability indicators.
- Research relevance: the tool supports scalable white-matter tractography quality control.
- Demo: [interactive tractography visualization](https://putiw.github.io/gallery/media/mri-afqview-hd.mp4).

### [Interactive 3D portfolio](https://putiw.github.io/)

Puti created a full-screen, explorable 3D portfolio that presents clinical application demonstrations, MRI and neuroimaging work, research posters, scientific figures, films, games, and artwork as a spatial gallery intended for human exploration.

### [Shrimp Tanks](https://putiw.github.io/shrimp-tanks/)

A browser-based shrimp simulation game created by Puti and included in the portfolio's game room.

## Research and publications

Puti earned a Ph.D. in Cognition and Perception from New York University in 2024. Her résumé lists five peer-reviewed journal articles, four as first author, plus 10+ conference abstracts and preprints.

- [Wen et al. (2025), “Single-trial fMRI decoding of 3D motion with stereoscopic and perspective cues,” *Journal of Neuroscience*](https://putiw.github.io/resume/#publication-motion-decoding). [Research poster](https://putiw.github.io/gallery/posters/decoding-detail.webp).
- [Wen et al. (2025), “Functional localization of visual motion area FST in humans,” *Imaging Neuroscience*](https://putiw.github.io/resume/#publication-fst). [VSS poster](https://putiw.github.io/gallery/posters/fst-detail.webp).
- [Enhanced Prediction of Multiple Sclerosis Disabilities Using Tract-Specific Lesion Load and Advanced Quantitative MRI Metrics](https://putiw.github.io/gallery/posters/ms-lesion-metrics-detail.webp), 2025 research poster.
- [MP2RAGE Ventricle Distance Profiling Improves Classification of Multiple Sclerosis Subtypes](https://putiw.github.io/gallery/posters/ohbm-pdi-detail.webp), OHBM 2025 poster.
- [CVS-View: AI-powered central vein sign identification](https://putiw.github.io/gallery/posters/menactrims-cvsview-detail.webp), MENACTRIMS 2025 poster.

## Canonical links and contact

- [Interactive 3D portfolio](https://putiw.github.io/)
- [Semantic HTML résumé](https://putiw.github.io/resume/)
- [Résumé PDF](https://putiw.github.io/Puti_Wen_Resume_2026.pdf)
- [GitHub](https://github.com/putiw)
- [LinkedIn](https://www.linkedin.com/in/puti-wen)
- [Google Scholar](https://scholar.google.com/citations?hl=en&user=tiJZLC4AAAAJ)
- [Email](mailto:pw1246@nyu.edu)

The root site is an immersive 3D research and software portfolio made for human exploration. Its application demos, posters, scientific figures, brain visualization, films, games, and artwork provide visual context beyond this factual summary.