Imaging methods have developed rapidly in recent decades, opening new opportunities for taxonomy and biodiversity studies of marine organisms. In particular, the microscopic size range, which used to be challenging to study due to time-consuming preparation and observation steps, now benefits from high throughput quantitative imaging methods and the development of fast high-resolution microscopy approaches. The dataset regroup raw images of three high resolution imaging methods applied to meiofauna samples with a focus on Nematoda taxa. This dataset from a semi automatized microscopy acquisition procedure and two 3D fluorescent microscopy protocols is linked to the publication entitled “Meiofauna investigation and taxonomic identification through imaging – a game of compromise” in Limnology and oceanography: Methods, 2025 were used.