This dataset supports the manuscript titled "Deep Learning Based Image Compression for Microscopy Images: An Empirical Study." The materials provided are essential for replicating the experiments in the study. The dataset is divided into three main parts: Config: train and test yaml config files for both 2D and 3D mmv_im2im labelfree task Sample_data: sample data to test the compression and the downstream labelfree code, in both 2D and 3D case. Model: fine-tuned 2D/3D labelfree model and 3D compression model. We use pre-trained 2D compression models from CompressAI