A High-Throughput Device for Consistent and Reproducible Wounds in In Vitro Scratch Assays: Introducing CellCut

1.0: Cell Cut 3.0 rendering

The in vitro scratch assay, also known as the wound healing assay, is a widely used method to study cell migration under controlled conditions. Despite its popularity, the reproducibility and scalability of scratch assays are often compromised by the manual nature of scratch generation, which typically relies on pipette tips or similar instruments. These approaches introduce variability in scratch width, depth, and location across wells and users. To address these limitations, we present CellCut—a precision-engineered, high-throughput wounding tool designed for reproducible scratch generation in multi-well plates. CellCut standardizes scratch creation across 48-well plates in a single motion, significantly reducing inter- and intra-experimental variability while increasing throughput and data quality. Alpha and Beta testing in academic and industrial laboratories has demonstrated positive results, with reduced time per assay, and high compatibility with automated imaging workflows. This article outlines the design, performance, and impact of CellCut on experimental reproducibility in cell migration research.

Scratch Assays Background

The study of cell migration is central to understanding physiological processes such as tissue regeneration, embryogenesis, and angiogenesis, as well as pathological processes like cancer metastasis, inflammation, and wound healing. One of the most accessible and cost-effective methods to assess migratory behavior is the in vitro scratch assay, where a physical wound is introduced into a confluent monolayer of cells, and the migration of cells into the wound area is quantified over time.

Despite its simplicity, the assay suffers from reproducibility issues due to the use of manual scratch tools—typically pipette tips or needles—that lack precision and standardization. Scratch width and location vary between users and even between wells within a single plate, introducing variability that can obscure biological insights and lead to inconsistent results. Additionally, manual scratching is time-consuming and incompatible with high-throughput workflows, limiting its scalability for screening applications.

Device Description: CellCut

CellCut is a novel wounding device engineered to eliminate the inconsistencies inherent in traditional scratch assay workflows. It features a simple 2-modules, top and bottom section, that fixes the plate in place and guides uniform scratches across all wells, optimized for compatibility with standard 48-well culture plates.

March to perfection

CellCut aims to enable precise, reproducible scratch formation across all wells in less than 30 seconds per plate. Compared to the pipette tip method, CellCut reduced scratch width variability by over 80%, improving the reliability of wound closure measurements over time. Moreover, edge morphology was more consistent, supporting automated segmentation and quantification using tools like ImageJ and CellProfiler.

Users also reported significant workflow improvements, including reduced fatigue, higher throughput, and improved alignment with automated imaging. These advantages position CellCut as an ideal solution for both low-volume academic labs and high-throughput industrial screening platforms.

Despite positive feedback, there are still first-time user pains, some degree of variability in scratches, slight user dependency, and performance variability within CellCut. Our team is actively working with our Beta tester partners and facilities to improve the device toward perfection.

Conclusion

While still in beta phase, CellCut device represents a major advancement in the execution of in vitro scratch assays, addressing long-standing issues with reproducibility, throughput, and user variability. By standardizing scratch creation, CellCut enables higher-quality data, improves experimental reliability, and supports broader adoption of scratch assays in wound healing, drug discovery, and cell migration research.

Applications and Use Cases

• Cancer metastasis studies

• Fibroblast and epithelial wound healing assays

• Stem cell migration research

• Drug screening and toxicology

• Regenerative medicine and biomaterials testing

  
  

Availability

CellCut is currently available through CLYTE’s First-Client Initiative, providing early access to qualifying laboratories for collaborative validation and feedback. To learn more or request a demonstration, visit https://www.clyte.tech/partnership