We have adapted the mouse kidney rudiment assay to generate renal organoids. We have immunostained endpoint fixed organoids and E13.5 embryonic kidneys and imaged them with a light sheet fluorescent microscope. The data generated for this manuscript is made accessible here and includes immunofluorescence staining after end point fixation revealing that organotypic structures develop within the organoids. Furthermore, we have performed an assay to ascertain tubular functionality. Following, we have imaged organoids containing Wt1-GFP knock-in...