Whole-slide Quantitative RNAscope Image Analysis: Applications and Methods


20th Apr 2022



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Date: 20 April 2022 (Wednesday)
Time: New York 11:00 | London 16:00 | Paris 17:00 | Singapore 23:00 | Tokyo 00:00 (21st April) | Sydney 01:00 (21st April)
Duration: 120 minutes
Event structure: Presentation + Q&A + Panel Discussion
Registration fee: Complimentary access
Webinar on-demand: Available to view until midnight 6 May 2022 (registration is required)


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!

Key discussion points:

• 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


 Time                                                              Title       Speaker
  11:00  Use of HALO Image Analysis Software for Quantification of RNAscope and Other ISH Studies     Dr. Julia Jones
  11:20  Cancer Associated Fibroblasts and Prostate Cancer Metastasis     Dr. Paula Hurley
  11:35  Spatial Organization Within the Tissue Microenvironment     Dr. Linda Nieman
  11:50  Question and Answer Session     ALL
  12:10  Panel Discussion    ALL


Get the full agenda

Presenters’ Details:

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

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.

Presentation 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.


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

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.

Presentation 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.


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

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.

Presentation 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).


Moderator Details:

Dr. Kim Collins – Scientific Marketing Manager, Indica Labs

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.


The meeting is free to attend
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Reuben Raj
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