ChAda-ViT : Channel Adaptive Attention for Joint Representation Learning of Heterogeneous Microscopy Image

Unlike color photography images, which are consistently encoded into RGB channels, biological images encompass various modalities, where the type of microscopy and the meaning of each channel varies with each experiment. Importantly, the number of channels can range from one to a dozen and their correlation is often comparatively much lower than RGB, as each of them brings specific information content. This aspect is largely overlooked by methods designed out of the bioimage field, and current solutions mostly focus on intra-channel spatial attention, often ignoring the relationship between channels, yet crucial in most biological applications. Importantly, the variable channel type and count prevent the projection of several experiments to a unified representation for large scale pre-training. In this study, we propose ChAda-ViT, a novel Channel Adaptive Vision Transformer architecture employing an Inter-Channel Attention mechanism on images with an arbitrary number, order and type of channels. We also introduce IDR-Cell100k, a bioimage dataset with a rich set of 79 experiments covering 7 microscope modalities, with a multitude of channel types, and counts varying from 1 to 10 per experiment. Our architecture, trained in a self-supervised manner, outperforms existing approaches in several biologically relevant downstream tasks. Additionally, it can be used to bridge the gap for the first time between assays with different microscopes, channel numbers or types by embedding various image and experimental modalities into a unified biological image representation. The latter should facilitate interdisciplinary studies and pave the way for better adoption of deep learning in biological image-based analyses. ‡ Code, Data & Model weights : https://github.com/nicoboou/chadavit Figure 1. Performance comparison on downstream tasks, showcasing ChAda-ViT's superiority in 6 out of 8 tasks compared to existing approaches[47] using CLS token only. R 2 scores, normalized to 0-100, are presented for BBBC021 Channel Reconstruction and Nuclear Translocation prediction tasks. This success is attributed to the combined use of Intra-Channel and Inter-Channel Attention. Evaluation on all tokens is detailled in Appendix. * The dataset can be accessed on Kaggle: CYCLoPs Dataset.