5282 Deep Learning Methods Powered by AI in Tissue Image Analysis

CIO Applications recently sat down with our founder and CEO Michael Grunkin. The technology print magazine focuses on usage of various tech s

From tedious manual annotation work to fully automated annotations with a streamlined image analysis workflow. This is now possible with AI tools that are remarkably accurate generating powerful results within tissue segmentation, cell identification, quantification and other cell-based tasks.


AI expands the possibilities in cancer research and diagnostics


Whether you are looking for nuclei quantification in IHC images, accurate tumor separation in H&E, or advanced context aware region mapping in brain images, Oncotopix®/Biotopix™ AI image analysis is your go-to toolbox. Deep neural networks bring virtually endless possibilities to augmented pathology.

AI made easy

The Oncotopix®/Biotopix™ AI platform is train-by-example image analysis for digital pathology, made easy-to-use. Deep learning convolutional neural algorithms are trained based on easily annotated training data provided by you as the user. AI is not magic – you are in control of the learned behavior.

Patented virtual double stain (VDS)

Are you already using Artificial Intelligence (AI) for image analysis in digital pathology, and have you experienced the time-consuming task of annotating enough training data to capture the variance in your images? Let Visiopharm introduce you to our unique patented Virtual Double Stain (VDS) method for automatic annotation of training data.

AI redefines what is possible in image analysis

In more advanced cases robust identification of morphologically and/or functionally distinct features in histological samples, such as glomeruli in the kidney, compartments of the brain, and tumor/stroma separation, continues to challenge traditional image analysis methods. Differences in disease severity; preanalytical variables, such as variance in staining intensity; and structures or regions reliant solely on context often result in tedious manual annotations to achieve necessary accuracy.

Stefan Hamann, PhD from the Translational Pathology Laboratory at Biogen has utilized Visiopharm’s context-based deep learning algorithms to automate the laborious manual tissue annotation process. The task involved sagittal mouse brain sections with 6 regions-of-interest. The result is a fully automated mouse brain annotation tool that is remarkably accurate when confronted with unique tissue artifacts, illuminating the possibilities of deep learning within a streamlined image analysis workflow.

Visiopharm’s AI webinar

Watch our webinar to experience Oncotopix®/Biotopix™ AI image analysis with real-life applications, where Visiopharm’s deep learning experts demonstrate the “how to” with explanations and relevant demo cases.

Visiopharm AI image analysis solution


The Oncotopix® and Biotopix™ AI image analysis modules are available and fully integrated with the Visiopharm current image analysis software platform. Visit visiopharm.com/ai-deeplearning

Visiopharm AI Image Analysis in the news

Please see the launch news at TissuePathology: Keith Kaplans Digital Pathology Blog

Categories: Blog | Comments 6253 Visiopharm & Fuidigm Co-promote Phenomap Image Analysis Software & Hyperion Imaging System

Fluidigm Announces Co-Marketing Agreement with Visiopharm to Expand and Simplify Imaging Mass Cytometry Data Analysis

Visiopharm Multiplex software presented at the Fluidigm Imaging Mass Cytometry User Group Meeting, expanding the suite of Hyperion Imaging System data analysis tools for translational and clinical research 

Fluidigm Corporation (NASDAQ:FLDM) and Visiopharm A/S today announced a co-marketing relationship to automate image analysis for Imaging Mass Cytometry™ (IMC™). Under the terms of this agreement, Fluidigm and Visiopharm will cooperatively promote Visiopharm® image analysis software in conjunction with the Fluidigm® Hyperion™ Imaging System, MCD™ Viewer software and related Maxpar® antibodies and kits.

Developed using proven Fluidigm CyTOF® technology, the Hyperion Imaging System surpasses the inherent limitations of fluorescence detection by using highly pure metal tags that are separated by mass instead of by wavelength. Setting a new standard in highly multiplexed protein detection, the system enables researchers to simultaneously detect up to 37 markers from a single tissue section by IMC. Providing comprehensive analysis of cellular phenotypes and their interrelationships within the spatial context of the tissue microenvironment, IMC is aiding researchers around the world to uncover meaningful new insights in health and disease.

We are committed to maximizing the full potential of mass cytometry to deeply interrogate tissue and tumor samples,” said Chris Linthwaite, President and CEO of Fluidigm. “Today we are excited to announce our agreement with Visiopharm, a leader in quantitative digital pathology software solutions. Together with Visiopharm, we are proud to bring new software capabilities to our growing IMC community.

On September 11, Visiopharm will present its Multiplex software at the Fluidigm Imaging Mass Cytometry User Group Meeting in Seattle. Developed as an expansion of the Oncotopix® Discovery platform, Multiplex enables researchers to perform automated analysis of images generated by the Hyperion Imaging System. Offered as a licensed software solution from Visiopharm, Multiplex provides automated cell segmentation and phenotyping of cell classes in addition to powerful visualization of cell populations with phenotypic charting and t-SNE clustering.

“The collaboration between Fluidigm and Visiopharm will provide scientists novel tools to understand the biology of cancer, including the phenotyping of cells within the tumor microenvironment,” said Michael Grunkin, CEO of Visiopharm. “Our complementary technologies provide an entirely new research approach to drive drug-diagnostic co-development on a tissue-based platform, with the potential to also provide a new framework for precision medicine in cancer.

Collaborating to provide high-value automated data analysis solutions for the Hyperion Imaging System is essential to our strategy to empower routine use of this powerful technology,” continued Linthwaite. “By introducing automation to the MCD™ Viewer analysis pipeline, Multiplex further expands the capabilities of the Hyperion Imaging System to advance our understanding of human disease and improve the future of care.

Fluidigme and Visiopharm Co Marketing Agreement2
Categories: Press Releases | Comments 6257 Visiopharm Becomes a Technology Leader in Deep Learning

Visiopharm Becomes a Technology Leader in Deep Learning and AI Image Analysis for Digital Pathology

Visiopharm Launches AI Powered by Deep Learning: Letting Pathologists Harness the Power of AI

The Oncotopix®/Biotopix™ AI image analysis platform is powered by the latest technological breakthroughs in AI and Deep Learning, providing the most comprehensive solution for image analysis available for Digital Pathology today.

With near infinite configurability, the Visiopharm AI software platform addresses even the most complex and challenging image analysis applications. This allows scientists and researchers to grow and evolve with their research without constantly hitting the walls of software limitations.

The intuitive “teach-by-example” implementation, makes it possible for pathologists to easily become proficient and generate highly accurate and reproducible results even if they have no skills in programming or advanced IT.

“Visiopharm really has become a leader in these types of deep learning methods which is really impressive” 

– Robert Dunstan, Senior Research Fellow, AbbVie

The deep learning technology in the Visiopharm AI image analysisplatform is specifically developed towards histopathology, so pathologists and scientists are able to apply, train and create high-quality deep learning algorithms to obtain breakthrough results in own field of work.

“Our AI platform was designed for offering the latest breakthrough advances in AI/Deep Learning Technology for Whole Slide Image Analysis in a way that enables immediate productivity with very little training, also for scientists with no IT-background; while still offering full configurability for experts,” said Michael Grunkin, CEO of Visiopharm. “This makes Oncotopix/Biotopix AI the ideal platform for tissue-based research: Scientists can grow with their research without experiencing limitations and barriers. We are excited to see how easy it is for our users to efficiently tackle applications that they weren’t able to address with other tools”.

“With these state-of-the-art deep learning algorithms optimized for tissue pathology, we see the second paradigm shift in AI for image analysis. We simply push the boundaries of what is possible in cancer research and drug development,” adds Jeppe Thagaard, deep learning research engineer, Visiopharm.

With the new AI image analysis platform, pathologists and scientists get the power of state-of-the-art deep learning to solve difficult problems – without having to write a single line of code. 

Watch Visiopharm’s AI webinar

Take a look and watch Visiopharm’s deep learning experts demonstrate the “how to” with explanations and demo cases relevant for nuclei quantification in IHC images, accurate tumor separation in H&E, and advanced context-aware region mapping in fx brain images. 

Watch the webinar here.

Visiopharm AI Image Analysis solution 

The Oncotopix® and Biotopix™ AI image analysis modules are available and fully integrated with the Visiopharm current image analysis software platform. Visit visiopharm.com/ai-deeplearning for details. 

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