ChE MS Thesis Defense: Benjamin Peck

Name: Benjamin Peck

Title: Generalizable Image Analysis Pipelines for Junction Fragmentation and Vascular Marker Analysis Applied to Blood-Brain Barrier Disease Models

Date: 03/26/2026

Time: 02:00:00 PM

Committee Members:
Prof. Eno Ebong (Advisor)
Prof. Abigail Koppes
Prof. Erel Levine
Rebecca Pinals

Location: East Village 102

Abstract:
Quantifying blood-brain barrier (BBB) integrity from fluorescence microscopy remains limited by subjective scoring and categorical classification methods that lack reproducibility. This thesis addresses these limitations by developing two semi-automated pipelines that replace manual scoring with automated, continuous-variable measurement of BBB-associated vascular markers in vitro and in vivo.

The in vitro pipeline, implemented in Python, quantifies tight junction fragmentation by measuring discrete zonula occludens-1 (ZO-1) fragment objects within manually traced junction regions, yielding continuous-variable metrics including average fragment area, junctional fragmentation ratio, and total junctional area. In human brain microvascular endothelial cells under glycocalyx knockdown (KD), the pipeline detected significantly reduced fragment area (37%, both p < 0.015) and junctional fragmentation ratio (both p < 0.014) in both CD44- and syndecan-1-KD conditions.

The in vivo pipeline integrates ilastik-based machine learning classification with FIJI macro automation to quantify vascular marker colocalization and resolves vessel signal from microglial contamination within a single fluorescence channel without requiring a dedicated counterstain. Applied across four mouse cohorts [young, aged, Alzheimer’s disease (AD), and traumatic brain injury (TBI)] and three brain regions (prefrontal cortex (PFC), hippocampus, and midbrain), the pipeline revealed concurrent ZO-1 loss and intercellular adhesion molecule-1 (ICAM-1) elevation in the PFC and hippocampus of aged and AD mice, with no significant differences between the two groups. Total endothelial nitric oxide synthase (eNOS) was the sole marker to show an AD-specific effect, nearly doubling in the PFC of AD mice (p = 0.0013). TBI mice showed persistent ZO-1 loss with transient changes in ICAM-1 and eNOS, consistent with published recovery timelines.

Both pipelines are deterministic, publicly available on GitHub, and designed for adoption beyond the specific markers and systems analyzed here.

Benjamin Peck is a second-year Master of Science candidate in Chemical Engineering at Northeastern University, expected to graduate in April 2026. His graduate research is conducted in the Ebong Mechanobiology Lab, where he investigates blood-brain barrier (BBB) dysfunction across Alzheimer’s disease, traumatic brain injury, and aging mouse models. His thesis, Generalizable Image Analysis Pipelines for Junction Fragmentation and Vascular Marker Analysis Applied to Blood-Brain Barrier Disease Models, centers on quantification of vascular markers in vitro and in vivo by examining tight junction integrity in cultured brain endothelial cells, and quantifying vascular marker expression across multiple brain regions and disease cohorts in mouse models, supported by custom image analysis pipelines developed for both. He received his B.S. in Chemical Engineering from Northeastern University in 2021. Prior to his graduate studies, Benjamin worked in industry across pharmaceutical and medical device settings. At Bristol Myers Squibb, he worked within the compound management departments at two Bay Area locations, supporting early-stage cardiovascular drug development through compound characterization and analytical testing. Before that, he worked at Genapsys, Inc. during the scale-up of a next-generation genomic sequencer, with responsibilities in quality systems and manufacturing operations. Benjamin’s industry background spans pharmaceutical, biotech, and medical device environments, with demonstrated expertise in analytical method development, quality systems, and workflow optimization. This fall, he will begin his doctoral studies, where he intends to continue investigating the mechanisms underlying vascular dysfunction and neurodegeneration.