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Multiparametric In Situ Imaging (MISI) Laboratory

In the era of precision medicine, we aim to help our patients by coupling extensive expertise in diagnostic tissue pathology with cutting-edge tools in order to comprehensively characterize tissue samples at the single cell level, thereby driving the discovery of novel and personalized therapies.

The Weill Cornell Medicine Department of Pathology and Laboratory Medicine established the Multiparametric In Situ Imaging (MISI) Laboratory in 2019 with the goal of centralizing within a CLIA-certified space both key personnel and several cutting-edge platforms, which are complementarily geared toward the in situ-based profiling of cellular microenvironments at single cell resolution, in tumor and non-tumor tissues. The MISI Lab is led by hematopathologist Sanjay Patel, M.D. and supported by the Center for Translational Pathology, Divisions of both Experimental and Computational Pathology. The following tools are currently available, and the lab is actively expanding: 

Vectra Polaris® Automated Quantitative Pathology Imaging System:

  • Simultaneous interrogation of up to 7 protein biomarkers
  • Fully automated workflow
  • High-throughput whole-slide/TMA imaging at 40x resolution




CO-Detection by indEXing (CODEX):

  • Simultaneous interrogation of up to 40 protein biomarkers
  • Ready-made immune monitoring panel (coming soon) or fully customized panel design




Nanostring GeoMX® Digital Spatial Profiler (DSP):

  • In situ/spatially-oriented interrogation of up to 30 protein biomarkers or ~1,800-18,000 RNA targets
  • Ready-made panels available or customized panel design
  • Computational pipelines for correlation with other single cell data



Key Services

  • Development of high-throughput, multiplex protein biomarker assays for clinical trial correlative studies or research investigation
  • Development of highly-multiplexed protein biomarker panels for exploratory research investigation and hypothesis generation
  • Comprehensive spatial gene expression profiling using formalin-fixed tissue samples
  • Pathologist-driven image analysis and data interpretation

Multiplex immunofluorescence panel performed on FFPE of mouse spleen using 6 markers (antibodies) + DAPI (nuclei, blue) and imaged using Vectra Polaris to illustrate normal tissue topography.

The image shown is a multiplex staining panel performed using Vectra Polaris on a human, Bouin-fixed, decalcified bone marrow core biopsy tissue sample.

Multiplex immunofluorescence panel performed on a tissue microarray (TMA) of prostate tumor samples.

MISI Staff

Sanjay Patel, MD is an Assistant Professor of Pathology and Laboratory Medicine based within the Division of Hematopathology. Prior to joining Weill Cornell, Sanjay completed his residency training in anatomic and clinical pathology at the University of Wisconsin Hospital and Clinics, followed by subspecialty clinical fellowship training and post-doctoral research in hematopathology at the Harvard Medical School, Brigham and Women’s Hospital and Dana-Farber Cancer Institute.

Paul Simonson, MD, PhD, is an Assistant Professor of Pathology and Laboratory Medicine based within the Division of Hematopathology. Prior to joining Weill Cornell, Paul completed his MD and PhD (physics) at the University of Illinois at Urbana-Champaign.  Graduate work focused primarily on development of nanometer-scale localization of fluorophores, two-photon microscopy, and super-resolution imaging in the laboratory of Paul Selvin.  Paul then went on to residency (anatomic and clinical pathology) and fellowship (hematopathology) at the University of Washington, where he also opted to stay for an extra research year, focusing on multiparametric CODEX imaging and machine learning techniques.

Ryan Carelli is a Staff Associate in the Department of Pathology and Laboratory Medicine who specializes in statistical and computational approaches to the analysis of imaging and genomics data. Prior to joining Weill Cornell, Ryan worked at Dana Farber Cancer Institute on prostate cancer tumor microenvironment, at Harvard Medical School on volumetric and super-resolution imaging, and at Boston College on optical methods in experimental condensed matter physics. 

Itzel Valencia, MS is a Research Technician in the Department of Pathology and Laboratory Medicine who performs full-stack multiparametric imaging experiments, from staining to imaging. Previously, Itzel worked at Columbia University Medical Center and received her Masters in Biology under Dr. Stephen Free at SUNY where she studied the synthesis of cell wall lichenin.


1: Stopsack KH, Huang Y, Tyekucheva S, Gerke TA, Bango C, Elfandy H, Bowden M, Penney KL, Roberts TM, Parmigiani G, Kantoff PW, Mucci LA, Loda M. Multiplex Immunofluorescence in Formalin-Fixed Paraffin-Embedded Tumor Tissue to Identify Single-Cell-Level PI3K Pathway Activation. Clin Cancer Res. 2020 Nov 15;26(22):5903-5913. Epub 2020 Sep 10. PMID: 32913135; PMCID: PMC7669556.

2: Patel SS, Lipschitz M, Pinkus GS, Weirather JL, Pozdnyakova O, Mason EF, Inghirami G, Hasserjian RP, Rodig SJ, Weinberg OK. Multiparametric in situ imaging of NPM1-mutated acute myeloid leukemia reveals prognostically-relevant features of the marrow microenvironment. Mod Pathol. 2020 Jul;33(7):1380-1388. PMID: 32051557.

3: Patel SS, Weirather JL, Lipschitz M, Lako A, Chen PH, Griffin GK, Armand P, Shipp MA, Rodig SJ. The microenvironmental niche in classic Hodgkin lymphoma is enriched for CTLA-4-positive T cells that are PD-1-negative. Blood. 2019 Dec 5;134(23):2059-2069. PMID: 31697809; PMCID: PMC7218752.

4: Hamid AA, Gray KP, Huang Y, Bowden M, Pomerantz M, Loda M, Sweeney CJ. Loss of PTEN Expression Detected by Fluorescence Immunohistochemistry Predicts Lethal Prostate Cancer in Men Treated with Prostatectomy. Eur Urol Oncol. 2019 Sep;2(5):475-482. PMID: 31411988.

5: Kabraji S, Sole X, Huang Y, Bango C, Sgroi D, Loda M, Ramaswamy S. AKT1low quiescent cancer cells in ductal carcinoma in situ of the breast. NPJ Breast Cancer. 2019 Mar 21;5:10. PMID: 30911675; PMCID: PMC6428812.

6: Huh SJ, Oh H, Peterson MA, Almendro V, Hu R, Bowden M, Lis RL, Cotter MB, Loda M, Barry WT, Polyak K, Tamimi RM. The Proliferative Activity of Mammary Epithelial Cells in Normal Tissue Predicts Breast Cancer Risk in Premenopausal Women. Cancer Res. 2016 Apr 1;76(7):1926-34. PMID: 26941287; PMCID: PMC4873436.

Cover image from a recent issue of Blood journal


Download the MISI Laboratory Fee Schedule here.

For inquiries and questions about the MISI Lab, please contact Sanjay Patel, MD, via email.

Weill Cornell Medicine Pathology & Laboratory Medicine 1300 York Avenue New York, NY 10065 Phone: (212) 746-6464 Fax: (212) 746-8192