Immunofluorescence images of iPSC-derived human intestinal organoids (HIOs), either mock-infected or infected with Ebola virus (EBOV) or Marburg virus (MARV), collected at Day 1 and Day 3 post-infection. These images correspond to Figure 6 in the associated manuscript. Fluorescent markers include GFP-CDX2 (green) for gut epithelial identity, EBOV NP or MARV NP (red) for viral nucleoprotein, and DAPI (blue) for DNA. Images were captured at 20x magnification for overall visualization and 63x magnification for detailed imaging of viral inclusion bodies. The dataset includes .tif files (some merged and some individual fluorescence channels used in the published figure panels), .czi files (multi-channel and z-stack raw microscopy data), and .gif files representing animated z-stack projections.