# CountPath: Automating Fragment Counting in Digital Pathology

arXiv: https://arxiv.org/abs/2503.10520 · HTML: https://mlsanity.com/paper/2503.10520/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 6 of its 18 references that are in the map.
- First posted on arXiv 13 Mar 2025.

## Builds on (most cited first, 6 of 6)

- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [DETRs Beat YOLOs on Real-time Object Detection](https://mlsanity.com/paper/2304.08069/) (2023)
- [YOLOv9: Learning What You Want to Learn Using Programmable Gradient Information](https://mlsanity.com/paper/2402.13616/) (2024)
- [YOLOv11: An Overview of the Key Architectural Enhancements](https://mlsanity.com/paper/2410.17725/) (2024)
- [LSM-YOLO: A Compact and Effective ROI Detector for Medical Detection](https://mlsanity.com/paper/2408.14087/) (2024)
- [Measuring agreement among several raters classifying subjects into one or more (hierarchical) categories: A generalization of Fleiss' kappa](https://mlsanity.com/paper/2303.12502/) (2023)

## Abstract (arXiv)

Quality control of medical images is a critical component of digital pathology, ensuring that diagnostic images meet required standards. A pre-analytical task within this process is the verification of the number of specimen fragments, a process that ensures that the number of fragments on a slide matches the number documented in the macroscopic report. This step is important to ensure that the slides contain the appropriate diagnostic material from the grossing process, thereby guaranteeing the accuracy of subsequent microscopic examination and diagnosis. Traditionally, this assessment is performed manually, requiring significant time and effort while being subject to significant variability due to its subjective nature. To address these challenges, this study explores an automated approach to fragment counting using the YOLOv9 and Vision Transformer models. Our results demonstrate that the automated system achieves a level of performance comparable to expert assessments, offering a reliable and efficient alternative to manual counting. Additionally, we present findings on interobserver variability, showing that the automated approach achieves an accuracy of 86%, which falls within the range of variation observed among experts (82-88%), further supporting its potential for integration into routine pathology workflows.