For example, images from two different satellites may both contain RGB channels, but the remaining channels can be different for each imaging source.

For example, images from two different satellites may both contain RGB channels, but the remaining channels can be different for each imaging source.

Prior work using Masked Autoencoders (MAEs) typically relies on random patch masking based on the assumption that images have significant redundancies across different channels, allowing for the reconstruction of masked content using cross-channel correlations. However, this assumption does not hold in Multi-Channel Imaging (MCI), where channels may provide complementary information with minimal feature overlap. Thus, these MAEs primarily learn local structures within individual channels from patch reconstruction, failing to fully leverage cross-channel interactions and limiting their MCI effectiveness. In this paper, we present ChA-MAEViT, an MAE-based method that enhances feature learning across MCI channels via four key strategies: (1) dynamic channel-patch masking, which compels the model to reconstruct missing channels in addition to masked patches, thereby enhancing cross-channel dependencies and improving robustness to varying channel configurations; (2) memory tokens, which serve as long-term memory aids to promote information sharing across channels, addressing the challenges of reconstructing structurally diverse channels; (3) hybrid token fusion module, which merges fine-grained patch tokens with a global class token to capture richer representations; and (4) Channel-Aware Decoder, a lightweight decoder utilizes channel tokens to effectively reconstruct image patches. Experiments on satellite and microscopy datasets, CHAMMI, JUMP-CP, and So2Sat, show that ChA-MAEViT significantly outperforms state-of-the-art MCI-ViTs by 3.0-21.5%, highlighting the importance of cross-channel interactions in MCI.

Multi-Channel Imaging (MCI) contains an array of challenges for encoding useful feature representations not present in traditional images. For example, images from two different satellites may both contain RGB channels, but the remaining channels can be different for each imaging source. Thus, MCI models must support a variety of channel configurations at test time. Recent work has extended traditional visual encoders for MCI, such as Vision Transformers (ViT), by supplementing pixel information with an encoding representing the channel configuration. However, these methods treat each channel equally, i.e., they do not consider the unique properties of each channel type, which can result in needless and potentially harmful redundancies in the learned features. For example, if RGB channels are always present, the other channels can focus on extracting information that cannot be captured by the RGB channels. To this end, we propose DiChaViT, which aims to enhance the diversity in the learned features of MCI-ViT models. This is achieved through a novel channel sampling strategy that encourages the selection of more distinct channel sets for training. Additionally, we employ regularization and initialization techniques to increase the likelihood that new information is learned from each channel. Many of our improvements are architecture agnostic and could be incorporated into new architectures as they are developed. Experiments on both satellite and cell microscopy datasets, CHAMMI, JUMP-CP, and So2Sat, report DiChaViT yields a 1.5-5.0% gain over the state-of-the-art.