arXiv subjects

Ulysses Balis

Publications and source records attributed to Ulysses Balis.

3 recordsLinked to original sources

arXiv2025

Iris: A Next Generation Digital Pathology Rendering Engine

Digital pathology is a tool of rapidly evolving importance within the discipline of pathology. Whole slide imaging promises numerous advantages; however, adoption is limited by challenges in ease of use and speed of high-quality image rendering relative to the simplicity and visual quality of glass slides. We introduce Iris, a new high-performance digital pathology rendering system. Specifically, we outline and detail the performance metrics of Iris Core, the core rendering engine technology. Iris Core comprises machine code modules written from the ground up in C++ and using Vulkan, a low-level and low-overhead cross-platform graphical processing unit application program interface, and our novel rapid tile buffering algorithms. We provide a detailed explanation of Iris Core's system architecture, including the stateless isolation of core processes, interprocess communication paradigms, and explicit synchronization paradigms that provide powerful control over the graphical processing unit. Iris Core achieves slide rendering at the sustained maximum frame rate on all tested platforms and buffers an entire new slide field of, view without overlapping pixels, in 10 ms with enhanced detail in 30 ms. It is able to buffer and compute high-fidelity reduction-enhancements for viewing low-power cytology with increased visual quality at a rate of 100-160 us per slide tile, and with a cumulative median buffering rate of 1.36 GB of decompressed image data per second. This buffering rate allows for an entirely new field of view to be fully buffered and rendered in less than a single monitor refresh on a standard display, and high detail features within 2-3 monitor refresh frames. These metrics far exceed previously published specifications, beyond an order of magnitude in some contexts. The system shows no slowing with high use loads, but rather increases performance due to cache mechanisms.

cs.GR↗

arXiv2025

The Iris File Extension

A modern digital pathology vendor-agnostic binary slide format specifically targeting the unmet need of efficient real-time transfer and display has not yet been established. The growing adoption of digital pathology only intensifies the need for an intermediary digital slide format that emphasizes performance for use between slide servers and image management software. The DICOM standard is a well-established format widely used for the long-term storage of both images and associated critical metadata. However, it was inherently designed for radiology rather than digital pathology, a discipline that imposes a unique set of performance requirements due to high-speed multi-pyramidal rendering within whole slide viewer applications. Here we introduce the Iris file extension, a binary container specification explicitly designed for performance-oriented whole slide image viewer systems. The Iris file extension specification is explicit and straightforward, adding modern compression support, a dynamic structure with fully optional metadata features, computationally trivial deep file validation, corruption recovery capabilities, and slide annotations. In addition to the file specification document, we provide source code to allow for (de)serialization and validation of a binary stream against the standard. We also provide corresponding binary builds with C++, Python, and JavaScript language support. Finally, we provide full encoder and decoder implementation source code, as well as binary builds (part of the separate Iris Codec Community module), with language bindings for C++ and Python, allowing for easy integration with existing WSI solutions. We provide the Iris File Extension specification openly to the community in the form of a Creative Commons Attribution-No Derivative 4.0 International license.

eess.IV↗

arXiv2018

Leveraging Clinical Time-Series Data for Prediction: A Cautionary Tale

In healthcare, patient risk stratification models are often learned using time-series data extracted from electronic health records. When extracting data for a clinical prediction task, several formulations exist, depending on how one chooses the time of prediction and the prediction horizon. In this paper, we show how the formulation can greatly impact both model performance and clinical utility. Leveraging a publicly available ICU dataset, we consider two clinical prediction tasks: in-hospital mortality, and hypokalemia. Through these case studies, we demonstrate the necessity of evaluating models using an outcome-independent reference point, since choosing the time of prediction relative to the event can result in unrealistic performance. Further, an outcome-independent scheme outperforms an outcome-dependent scheme on both tasks (In-Hospital Mortality AUROC .882 vs. .831; Serum Potassium: AUROC .829 vs. .740) when evaluated on test sets that mimic real-world use.

cs.LG↗