Neha Koottumakkal Mohanan

Projects 1. Alzheimer’s Disease Sequencing Project (ADSP)

• Tools: Python, Pandas, DICOM, Bash, Excel, VS Code and GitHub Copilot
  Datasets: ADNI, OASIS3, NACC, UKBB, SCAN, AIBL
• Downloaded and preprocessed image data alongside clinical and biomarker information.
• Processed and integrated multimodal clinical datasets, including demographic details, cognitive status, cognitive scores, and scan data, with corresponding MRI image data.
• Designed a data structure model from raw data and performed table merging focused on T1-weighted (T1w) MRI images.
• Linked image metadata and calculated scan-level features such as age at scan and modality type.
• Conducted large-scale image quality assessments and generated structured Excel reports for flagged scans.
• Visualized over 18,000 MRI scans using custom Python pipelines to detect anomalies (e.g., blank images, orientation issues).
• Conducted subplot-based MRI image analysis and managed storage on the server
• Automated preprocessing and data cleaning using Bash scripts and custom directory management tools.
• Delivered multiple curated dataset versions to support downstream analysis and model development.
• Developed scripts using VS Code and GitHub Copilot for data processing, server-side data management, and analysis workflows.

Project 2: Early Brain Tumor Detection

• Tools: Python, Nibabel, Matplotlib
  Datasets: Glioblastoma (GBM), Stroke, Psychiatric cohorts
• Analyzed the structure of GBM, stroke, and psychiatric imaging datasets.
• Selected relevant MRI series using Series Description metadata for registration.
• Developed Python scripts to explore, clean, and visualize imaging data, including blank scan detection.
• Organized flagged images into review folders and visualized slices using subplots.
• Created structured DataFrames to support further analysis and machine learning workflows.

• Clinical Data Analysis
• MRI analysis using Matlab
• Developing codes for reading/ analyzing/ Optimizing of Dynamic susceptibility contrast(DSC) brain Magnetic Resonance Perfusion data.
• Perfusion analysis for digital reference object(DRO) insilico data.
• Quantifying tissue characteristics using smash/Qupath image analysis software's.