Online narrative guides for illuminating tissue atlas data and digital pathology images

Abstract

The recent introduction of highly multiplexed imaging of human tissues and tumors promises to fundamentally advance research in tissue biology and human disease. At the same time, histopathology in the clinical setting is undergoing a rapid transition to digital methods. Thus, repositories of imaging data from research and clinical specimens will soon join genomic databases as a means to systematically explore the molecular basis of disease. Even with recent advances in machine learning, experience in anatomic pathology has shown that there is no substitute for expert visual review, annotation, and description of image data. We review the ecosystem of software available for atlas and histopathology images and introduce a new Web-based software tool, Minerva Story, that addresses a critical unmet need. Minerva is an interpretative and interactive guide to complex images organized around guided analysis. We discuss how Minerva and similar software will be integrated into multi-omic browsers for data dissemination of future atlases.

The spatial landscape of progression and immunoediting in primary melanoma at single cell resolution

“…Brief Description of MINERVA. MINERVA (Hoffer et al, 2020;Rashid et al, 2020) enables intuitive real-time exploration of very large (gigapixel) high-plex images on the cloud using a web browser. With MINERVA, users can pan around and magnify areas of an image and switch between channels.…”

Visual cohort comparison for spatial single-cell omics-data

“…In our previous work on ImaCytE [48], we propose an interactive exploratory pipeline for cell type identification and neighborhood analysis in spatial single-cell data. Minerva [41] extends such exploration concepts with storytelling tools, to support communication and sharing of results. All of the above focus on the identification or exploration of cell types or significant multi-cellular interactions in a single cohort of spatial single-cell data.…”

Pancreatlas: Applying an Adaptable Framework to Map the Human Pancreas in Health and Disease

“…31 Finally, we are cognizant of the need to communicate biomedical research beyond the academic community, and we are exploring ways to make Pancreatlas more approachable to those without domain-specific knowledge. For example, the recently developed tool Minerva from Rashid and colleagues 32 represents an exciting opportunity to incorporate narrative guides into the presentation of histological images. Software tools such as this one could be utilized to highlight unique aspects of individual datasets and image collections.…”