MorphoHELM: A Comprehensive Benchmark for Evaluating Representations for Microscopy-Based Morphology Assays
Quick Take
MorphoHELM is a new benchmark for evaluating microscopy-based feature extraction methods in Cell Painting assays.
Key Points
- Consolidates evaluation standards for microscopy representations.
- Assesses methods under varying levels of technical noise.
- Publicly available datasets and tools for researchers.
📖 Reader Mode
~2 min readAbstract:Microscopy images contain rich information about how cells respond to perturbations, making them essential to applications like drug screening. To quantify images, researchers often use representation extraction methods, and recent years have seen a proliferation of deep learning methods. While measuring the quality of these representations is essential, evaluation remains fragmented, with each proposed model evaluated on different tasks and datasets, using custom pipelines and metrics, making it difficult to fairly compare models. Here, we introduce MorphoHELM, a comprehensive open benchmark for evaluating feature extraction methods for Cell Painting, the most widely-used morphological profiling assay. MorphoHELM consolidates evaluation standards in the field, extends and corrects them to be more robust, and evaluates on the widest range of methods to date. A defining feature of the benchmark is that each task is evaluated at different degrees of batch effects (or technical noise), directly quantifying how the ability of methods to detect biological signal degrades as noise increases. Together, these properties enable MorphoHELM to detect trade-offs between methods, and we demonstrate that models that excel at certain kinds of biological signal are weaker at others. We show that no existing model outperforms classic computer vision analytic strategies across all settings, which remain the strongest general use-case representations. All datasets, code, and evaluation tools are publicly available at this https URL.
| Subjects: | Computer Vision and Pattern Recognition (cs.CV) |
| Cite as: | arXiv:2605.15383 [cs.CV] |
| (or arXiv:2605.15383v1 [cs.CV] for this version) | |
| https://doi.org/10.48550/arXiv.2605.15383 arXiv-issued DOI via DataCite (pending registration) |
Submission history
From: Emre Berk Hayir [view email]
[v1]
Thu, 14 May 2026 20:13:36 UTC (544 KB)
— Originally published at arxiv.org
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