# Optimization of whole slide imaging scan settings for computer vision using human lung cancer tissue

## TL;DR

This study finds the best settings for scanning lung cancer tissue to create high-quality images for computer vision analysis.

## Contribution

The paper identifies optimal scan settings that balance image quality and efficiency for digital pathology.

## Key findings

- High general matching percentages were observed between scans, but replicate similarity was low.
- Longer scanning times and larger data volumes did not improve replicate similarity.
- Optimal settings combined consistent performance with reduced scanning time.

## Abstract

Digital pathology has become increasingly popular for research and clinical applications. Using high-quality microscopes to produce Whole Slide Images of tumor tissue enables the discovery of insights into biological aspects invisible to the human eye. These are acquired through downstream analyses using spatial statistics and artificial intelligence. Determination of the quality and consistency of these images is needed to ensure accurate outcomes when identifying clinical and subclinical image features. Additionally, the time-intensive process of generating high-volume images results in a trade-off that needs to be carefully balanced. This study aims to determine optimal instrument settings to generate representative images of pathological tissue using digital microscopy. Using various settings, an H&E stained sample was scanned using the ZEISS Axio Scan.Z1. Next, nucleus segmentation was performed on resulting images using StarDist. Subsequently, detections were compared between scans using a matching algorithm. Finally, nucleus-level information was compared between scans. Results indicated that while general matching percentages were high, similarity between information from replicates was relatively low. Additionally, settings resulting in longer scanning times and increased data volume did not increase similarity between replicates. In conclusion, the scan setting ultimately deemed optimal combined consistent and qualitative performance with low throughput time.