Abstract
Choosing a deep learning architecture for label-free single-cell classification remains an open question, with microscopy benchmarks reporting conflicting conclusions about CNNs versus transformers. We present a controlled benchmark on LIVECell phase-contrast microscopy data using source-image-disjoint train/validation/test splits to prevent parent-image leakage and matched optimisation, augmentation, and evaluation protocols across EfficientNet, Vision Transformer (ViT), and EVA-02 models. This allows the effects of architecture, pretraining, fine-tuning, tokenisation, and distillation to be disentangled. We find that the previously reported CNN advantage is largely explained by pretraining rather than architecture: the smallest pretrained model outperforms the strongest model trained from scratch despite far fewer parameters. Pretraining improves macro-F1 by 3-4 points, while the gap between the best pretrained CNN and transformer is below 0.5 points. Architectural choices nevertheless matter: ViT-S/8 outperforms ViT-S/16 and matches the four-times-larger ViT-B/16 at a quarter of the parameters, showing that finer tokenisation benefits small cell crops. Conversely, layer-wise learning-rate decay, central to the EVA-02 fine-tuning recipe, degrades performance, highlighting that transfer heuristics from natural-image recognition may not generalise to microscopy. Finally, knowledge distillation substantially improves the deployment frontier: compact EfficientNet-B0 students distilled from teacher councils outperform every individually trained backbone, including the EfficientNet-B5 and EVA-02 teachers. Overall, our results show that rigorous control of pretraining and evaluation is essential for interpreting biomedical architecture benchmarks, while distillation may be a more effective route to practical single-cell classification than architecture choice alone.
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Apr 13, 2026cs.CV
Background: Task-specific microscopy datasets are often small, making it difficult to train deep learning models that learn robust features. While self-supervised learning (SSL) has shown promise through pretraining on large, domain-specific datasets, generalizability across datasets with differing staining protocols and channel configurations remains underexplored. We investigated the generalizability of SSL models pretrained on ImageNet-1k and HPA FOV, evaluating their embeddings on OpenCell with and without fine-tuning, two channel-mismatch strategies, and varying fine-tuning data fractions. We additionally analyzed single-cell embeddings on a labeled OpenCell subset. Result: DINO-based ViT backbones pretrained on HPA FOV or ImageNet-1k transfer well to OpenCell even without fine-tuning. Fine-tuning further improved performance to 0.704
± 0.027 (17 classes, multi-class labels). At the single-cell level, the HPA single-cell-pretrained model achieved the highest k-nearest neighbor performance across all neighborhood sizes (macro
F1 ≥ 0.515). Conclusion: SSL methods like DINO, pretrained on large domain-relevant datasets, enable effective use of deep learning features for fine-tuning on small, task-specific microscopy datasets.
Ben Isselmann, Dilara Göksu, Heinz Neumann +1
Jul 5, 2026cs.CV
Hierarchical structure is common in image data, where fine-grained clusters often merge into larger, coarser semantic groups. In biological cell images, current self-supervised learning models often suppress this hierarchy, as coarse factors such as imaging modality can obscure finer morphological attributes in the latent space. We propose a hierarchy-aware self-supervised training framework to address this problem. Our method combines two components: a distillation framework with a segmentation teacher to improve morphological awareness in the latent space, and a hierarchy-aware contrastive loss based on HDBSCAN to improve decision boundaries between closely related subtypes at different hierarchical levels. Together, these components reduce the tendency of self-supervised learning to overemphasize coarse factors and instead align embeddings with semantic and morphological cues. This yields biologically meaningful sub-clusters driven by fine morphological detail. We train and evaluate our method on a curated corpus of 2.3 million single cells aggregated from 20 microscopy datasets, both labeled and unlabeled, covering 208 cell classes. Our method improves over baseline and counterpart methods, increasing average top-K accuracy by 2.8%, top-9 retrieval on the dataset with the deepest hierarchy by 6.3%, and downstream F1-score for biologically relevant drug classification from perturbed cell morphology by 7.8%.
Julius Riel, Vishwa Mohan Singh, Sai Anirudh Aryasomayajula +10
Jul 20, 2026q-bio.GN
Large single-cell datasets are expensive to store, curate, and repeatedly reuse for model training. Data distillation can reduce this burden by building smaller training sets. However, many existing methods rely on synthetic cells. These synthetic cells do not retain direct correspondence with assayed cells and genes. This limits source-level inspection and biological traceability. Moreover, real-cell expression matrices are often sparse and noisy. In light of these challenges, we propose Minmax-CF, a label-aware characteristic-function selector for traceable single-cell data distillation. Minmax-CF formulates compression as a discrete min--max selection problem over characteristic-function directions. It uses entropy-regularized maximization to emphasize the least preserved directions. Greedy minimization ranks cells and genes by how much they reduce the resulting weighted error. The method alternates cell and gene selection under explicit axis-specific budgets. Across five coarse-lineage benchmarks and five compression budgets, Minmax-CF retains 95.3% of the Full-reference macro-F1 on average, with gaps that exceed one per-seed standard deviation. It also retains exact source-cell indices and original gene symbols. Compared with size-matched synthetic PCA-Centroid and Distribution Matching (DM) baselines, Minmax-CF achieves higher coarse-lineage macro-F1 in 24 of 25 comparisons against each baseline. It exceeds their average performance by 10.4% and 17.4%, respectively. Retained cells can also be projected onto independently computed embeddings for direct biological interpretation.
Yaodi Luo, Peize He, Lingbei Meng +4