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Denis Schapiro

Publications and source records attributed to Denis Schapiro.

3 recordsLinked to original sources

How Spatial Biologists Direct and Verify AI-Assisted Analyses

Spatial biologists use visualization to assess computational analyses of tissue data. We examine how they direct and verify analyses when an AI agent performs this work. We synthesized workflows from fourteen contextual inquiries and conducted a formative pilot followed by an observational study with ten spatial biologists using Claude Science on their own data. Participants valued help with plotting, locating cells of interest, and tasks they found laborious or could not otherwise perform. Assessing the agent's work involved obtaining suitable evidence, sometimes through additional work in external tools, and interpreting it using knowledge of the tissue and its markers. Scientists also sought information about ongoing computation to decide how analysis should proceed. We contribute a workflow synthesis, an empirical account of scientists directing and verifying agentic analyses, and four design directions addressing execution control, familiar interactive views, source and execution information, and accessible verification across computing setups and experience.

cs.HC↗

Harmonizing the Generation and Pre-publication Stewardship of FAIR Image Data

Alongside molecular insights into genes and proteins, biological imaging holds great promise for deepening scientific understanding of complex cellular systems and advancing predictive, personalized therapies for human health. To realize this potential, quality-assured image data must be shared globally across laboratories to enable comparison, pooling, and reanalysis-unlocking value far beyond the original purpose of data collection. Two broad sets of requirements are essential to enable image data sharing in the life sciences. The companion article Enabling Global Image Data Sharing in the Life Sciences outlines the need to develop cyberinfrastructure for sharing bioimage data. In this manuscript, we detail a broad set of requirements, which involves collecting, managing, presenting, and propagating contextual information essential to assess the quality, understand the content, interpret the scientific implications, and reuse bioimage data in the context of the experimental details. We start by providing an overview of the main lessons learned to date through international community activities, which have recently made considerable progress toward generating community standard practices for imaging Quality Control (QC) and metadata. We then provide a clear set of recommendations for amplifying this work. The driving goal is to address remaining challenges and democratize access to everyday practices and tools for a spectrum of biomedical researchers, regardless of their expertise, access to resources, and geographical location.

q-bio.OT↗

MITI Minimum Information guidelines for highly multiplexed tissue images

The imminent release of tissue atlases combining multi-channel microscopy with single cell sequencing and other omics data from normal and diseased specimens creates an urgent need for data and metadata standards that guide data deposition, curation and release. We describe a Minimum Information about highly multiplexed Tissue Imaging (MITI) standard that applies best practices developed for genomics and other microscopy data to highly multiplexed tissue images and traditional histology.

q-bio.OT↗