Our thoughts on the recent Visiopharm updates (version 2024.07)

It's been an exciting past year within the digital pathology field at OracleBio, with the ever-increasing interest in highplex immunofluorescence (IF) analysis and the generation of complex and meaningful data to support R&D pipelines for pharma and biotech.? Such work has challenged our experienced team of image analysis scientists to think outside of the box and develop innovative solutions while maintaining the robustness and our high standards of work.

The software we use is a crucial component of our end-to-end image analysis workflows. It needs to be stable enough to handle our high volume of AI algorithm training and analysis while still maintaining flexibility to answer the more niche biological questions. As another year has passed, Visiopharm has released the much-anticipated software version 2024.07, equipping our scientists with more tools and updates to help advance and optimise our standardised image analysis workflows.

Below are some of our favourite updates to the software that we're thrilled to share.?

Streamlined Image Analysis Workflow

Over the last year, a notable change to the software has been the continual refinements being made to the user interface, aiming to create a more streamlined process for users. A small but impactful update has been the changes implemented into the Colour Adjustment Menu. In highplex analyses, our scientists often wish to update image channel names for conciseness or clarity during algorithm development – and Visiopharm have listened! With the recent update, we can now create configurations with updated channel names which will carry through to the APP Author and Colour Adjustment Menu when we review analysis overlays.

On a similar note, this update has introduced the ability to specify colours for in-APP features, a great change to help improve how we will visualise custom-developed features for complex image analysis needs!?

Phenoplex Guided Workflow – Spatial Analysis Tools

By far, the most exciting feature of the update is the new spatial analysis tools implemented into the Phenoplex Guided Workflow. To meet the increasing demand for spatial phenotyping, Visiopharm has added two new modules: 1) ?Neighbourhood Counts and 2) Nearest Neighbour calculations. Using the workflow, threshold sets can be easily defined and adjusted in combination with the Colour Adjustment Menu to swiftly and accurately assess positivity levels per marker. Once these thresholds have been reviewed – using the co-occurrence matrix and phenotype list – and applied to any other images, the spatial analysis modules can now vastly extend the data we can extract from such images. Both modules offer our scientists the ability to fine-tune the spatial calculations we wish to perform in an easily scalable way, as shown below.

The intuitive toolset now enables our scientists to not only calculate intricate spatial calculations but visualise these in an interactive workflow to review and explore the data. Combined with the continually evolving data QC tools offered on the software, users can regularly review and visualise the data to trust the results we generate. ?

Figure (above): Demonstration of the Phenoplex Guided Workflow and spatial analysis.

• A) Example fields of view (n=3) of a 5-plex IF image, with a tumour ROI (blue) and stroma ROI (red).
• B) Visualisation of all phenotypes identified once thresholds have been defined.
• C) Spatial analysis highlighting CD3? CD8? cytotoxic T-cells (yellow) within 10μm of CD68? macrophages (pink).

Thanks to software like Visiopharm, OracleBio is equipped with essential tools to deliver insightful and meaningful data for our Clients’ diverse and niche multiplex image analysis requests. OracleBio’s strong working relationship with Visiopharm and the R&D teams helps provide insight into features during the development pipeline, creating a productive shared learning environment.

Moving forward, we cannot wait to continue collaborating with Visiopharm, R&D teams within pharma and biotech, and our Clients to exemplify why OracleBio is one of the global leaders in the evolving field of quantitative digital pathology.

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This article was written by OracleBio Senior Image Analysis Scientist Matthew McFarlane.