Method and system for trans-illumination imaging. In an exemplary method, a sample is irradiated in a well. The sample may include biological cells and a liquid or semi-solid medium that forms a meniscus. The step of irradiating may be performed with an array of light sources generating light of respective light beams that are incident on the meniscus at different orientations from one another. One or more images may be detected. A proportional contribution of light from two or more subsets of the light sources to the one or more images may be controlled by differential energization of the two or more subsets relative to one another to compensate for refraction by the meniscus and improve contrast.