A sample observation device comprising a sample container having a membrane filter, the sample observation device being configured to observe a sample held in the sample container having a first sample holding space and a second sample holding space partitioned by the membrane filter, the sample observation device comprising: an irradiation optical system configured to irradiate the sample with planar light along a first direction being a Z-axis, the planar light (L2, L2a) including a wavelength that is transmitted through the membrane filter as excitation light; a scanning unit configured to scan the sample along a second direction being an Y-axis orthogonal to the first direction with respect to an irradiation surface for the planar light (L2, L2a), the irradiation surface being a surface within a plane XZ defined by the first direction and a third direction being an X-axis orthogonal to the first direction and the second direction; an imaging unit configured to image observation light including fluorescent light generated due to the irradiation with the planar light and to output fluorescent light image data (G, G1) based on an imaging result, the fluorescent light image data (G,G1) corresponding to an image of the fluorescent light generated on the irradiation surface for the planar light (L2,L2a) on the XZ plane; an image formation optical system that has an observation axis inclined with respect to the irradiation surface and is configured to form an image of the observation light on the imaging unit; wherein a fluorescent light image (Ml) corresponding to the sample located in the first sample holding space and a fluorescent light image corresponding to the sample located in the second sample holding space can appear in the fluorescent light image data (G, G1); a partial image generation unit configured to specify a first area corresponding to the first sample holding space and a second area corresponding to the second sample holding space in the fluorescent light image data (G,G1), and to generate first partial image data corresponding to the first area and second partial image data corresponding to the second area; an observation image generation unit configured to generate first observation image data on the basis of the first partial image data and to generate second observation image data on the basis of the second partial image data; an analysis unit configured to analyze the sample on the basis of the first observation image data and the second observation image data; and wherein the scanning unit includes a moving stage configured to move the sample container that holds the samples; the moving stage is configured to scan the sample container along the second direction within a plane orthogonal to the optical axis of the planar light (L2, L2a) and scanning and imaging of the sample can be simultaneously performed. an irradiation optical system configured to irradiate the sample with planar light along a first direction being a Z-axis, the planar light (L2, L2a) including a wavelength that is transmitted through the membrane filter as excitation light; a scanning unit configured to scan the sample along a second direction being an Y-axis orthogonal to the first direction with respect to an irradiation surface for the planar light (L2, L2a), the irradiation surface being a surface within a plane XZ defined by the first direction and a third direction being an X-axis orthogonal to the first direction and the second direction; an imaging unit configured to image observation light including fluorescent light generated due to the irradiation with the planar light and to output fluorescent light image data (G, G1) based on an imaging result, the fluorescent light image data (G,G1) corresponding to an image of the fluorescent light generated on the irradiation surface for the planar light (L2,L2a) on the XZ plane; an image formation optical system that has an observation axis inclined with respect to the irradiation surface and is configured to form an image of the observation light on the imaging unit; wherein a fluorescent light image (Ml) corresponding to the sample located in the first sample holding space and a fluorescent light image corresponding to the sample located in the second sample holding space can appear in the fluorescent light image data (G, G1); a partial image generation unit configured to specify a first area corresponding to the first sample holding space and a second area corresponding to the second sample holding space in the fluorescent light image data (G,G1), and to generate first partial image data corresponding to the first area and second partial image data corresponding to the second area; an observation image generation unit configured to generate first observation image data on the basis of the first partial image data and to generate second observation image data on the basis of the second partial image data; an analysis unit configured to analyze the sample on the basis of the first observation image data and the second observation image data; and wherein the scanning unit includes a moving stage configured to move the sample container that holds the samples; the moving stage is configured to scan the sample container along the second direction within a plane orthogonal to the optical axis of the planar light (L2, L2a) and scanning and imaging of the sample can be simultaneously performed.