Whole-slide Quantitative RNAscope Image Analysis: Applications and Methods

Date: 20 April 2022
Time: 8:00 – 9:00 PST | 11:00 – 12:00 EST | 16:00 – 17:00 GMT
Location: Webinar

In this 2-hour event, learn from three experts in RNAscope image analysis with HALO® as they present their scientific research, share RNAscope tips and tricks, and participate in a panel discussion.
Agenda (EDT)
Time Title Speaker
Use of HALO Image Analysis Software for Quantification of RNAscope and Other ISH Studies
Dr. Julia Jones
Cancer Associated Fibroblasts and Prostate Cancer Metastasis
Dr. Paula Hurley
Spatial Organization Within the Tissue Microenvironment
Dr. Linda Nieman
Question and Answer Session
Panel Discussion


Join us for this 2-hour event, where three experts in RNAscope quantification across whole slide tissues present their research using the HALO image analysis platform from Indica Labs.

Dr. Julia Jones of Cancer Research UK will present an introduction to using HALO image analysis software for quantification of RNAscope and other ISH assays. Dr. Paula Hurley of Vanderbilt University Medical Center will present research using multiplex RNAscope image analysis to identify a subset of cancer associated fibroblasts associated with cribiform prostate cancer and worse oncologic outcomes. Dr. Linda Nieman of the Translational Imaging Core at Massachusetts General Hospital will present work combining RNAscope assays with HALO software to identify spatially organized cells that act in concert to form tumor immunity hubs in colorectal cancer.

Following the HALO customer presentations, a panel discussion on addressing common challenges of RNAscope image analysis follows. Be sure to bring your RNAscope image analysis questions to this event!

Learning Objectives

  • Learn about image analysis options for quantification of RNAscope and other ISH assays in HALO  
  • Learn how to combine RNAscope assays with spatial analysis in HALO to investigate tumor immunity hubs in colorectal cancer
  • Learn about quantitative RNAscope image analysis in cribiform prostate cancer
  • Hear from RNAscope image analysis experts on addressing common challenges


Dr Julia Jones
Scientific Manager of Histopathology/ISH Core Facility, Cancer Research UK/Cambridge Institute,
University of Cambridge​

Title: Use of HALO Image analysis software for quantification of RNAscope and other ISH studies

Abstract: I will give an introduction to the Histopathology/ISH Core Facility at the Cancer Research UK Cambridge Institute and an overview of the different RNAscope assays we offer for researchers. We also advise on and perform image analysis of RNAscope and other ISH techniques using HALO software and I will show a few examples and give recommendations for how to overcome some common issues.

Biography: Julia has a BSc Biomedical Science from Southampton University and a PhD in Neuroscience from University of Cambridge (Babraham Institute) and has experience in the Pharmaceutical Industry at Eli Lilly and GlaxoSmithKline.

Julia joined CRUK-Cambridge Institute (CI) Histopathology/ISH core facility at the beginning of 2007 as a Scientific Officer and set up the In Situ Hybridisation service. Julia is now the Scientific Manager for ISH and line manages two members of staff. Current methods offered by the ISH Service include automated branched-DNA ISH for detection of messenger RNA and non-coding RNA, Locked Nucleic Acid ISH for detection of microRNA, and FISH for detecting DNA. The service also offers two different methods for detecting single nucleotide polymorphisms in RNA.

Julia is co-organiser of the biennial symposium: Applications of In Situ Hybridisation in Research and Disease.

Dr. Paula Hurley
Associate Professor,
Vanderbilt University Medical Center​

Title: Cancer Associated Fibroblasts and Prostate Cancer Metastasis

Abstract: Cribriform prostate cancer is an aggressive histological subtype of prostate cancer that is associated with progression to lethal disease. While much research has focused on cancer cell intrinsic factors, less is known about how the tumor microenvironment contributes to cribriform prostate cancer aggressiveness. This study used single-cell RNA sequencing and multiplex RNAscope paired with HALO Software of patient samples to identify a subset of cancer associated fibroblasts (CAF) associated with cribriform prostate cancer and worse oncologic outcomes. In vivo functional studies showed the involvement of these CAFs in metastatic progression. Collectively, these studies have identified a cell type in the tumor microenvironment that mediates prostate cancer metastasis.      

Biography: Paula Hurley, PhD is an Associate Professor in the Division of Hematology and Oncology in the Department of Medicine at Vanderbilt University Medical Center (VUMC) and the Vanderbilt-Ingram Cancer Center. She is a co-leader of professional development in Hematology and Oncology as well as a co-leader of Vanderbilt Interdisciplinary Prostate Research. She obtained her PhD from the University of Chicago and did her post-doctoral training at Johns Hopkins University where she was retained as faculty. Due to her expertise in prostate cancer research, she was recently recruited to VUMC. Her research focuses on the tumor microenvironment, mechanisms of metastasis, and therapeutic resistance in prostate cancer. Her current research is supported by both governmental and private foundation grants.

Dr. Linda Nieman
Director of CCR Translational Imaging Core and Senior Scientist
Massachusetts General Hospital Cancer Center ​

Title: Spatial organization within the tissue microenvironment

Abstract: Great strides have been made in understanding disease with bulk tissue and single cell sequencing methods. The missing piece to the puzzle is the spatial relationship that connects the diverse component parts. A whole slide image of tissue with multiple biomarker labels is a snapshot in time that can be leveraged to understand the interplay of different cell types. I will present work combining RNAscope assays with HALO software to identify spatially organized cells that act in concert to form tumor immunity hubs in colorectal cancer (CRC).

Biography: Linda T Nieman is the Director of Translational Imaging Core at the Massachusetts General Hospital, Cancer Center. Dr. Nieman’s work focuses on applying digital pathology and computational methods to advance cancer research and improve patient care. As a senior scientist, Dr. Nieman works in close partnership with researchers and physician scientists to explore basic biology as well as develop solutions that address clinical needs. Dr. Nieman has special interest in spatial approaches to reveal the careful coordination of cells within the tissue microenvironment. Dr. Nieman received her PhD in Physics from The University of Texas at Austin.

Moderator: Dr. Kim Collins
Scientific Marketing Manager
Indica Labs ​

Biography: Kim Collins, PhD is a Scientific Marketing Manager at Indica Labs. In her current role, she is responsible for managing co-marketing partnerships, management of scientific presentations at conferences, webinars, and creation of scientific content such as application notes and white papers. Kim completed her undergraduate work at the University of California, San Diego in Biochemistry and Cell Biology, and obtained her PhD from the University of Washington and Fred Hutchinson Cancer Research Center Molecular and Cellular Biology Program where she developed a passion for microscopy. In her postgraduate work at the Stowers Institute of Medical Research, she continued to use high and super resolution microscopy to advance her research. ​

Scroll to Top