An image sensor integrated circuit may contain image sensor pixels. A channel containing a fluid with particles such as cells may be formed on top of the image sensor. Some of the image sensor pixels may form a calibration sensor and some of the image sensor pixels may form an imager. As the fluid and particles flow through the channel at a flow rate, the calibration sensor may measures the flow rate and illumination intensity in the channel. Based on calibration data such as measured flow rate and measured illumination intensity, adjustments may be made to ensure that the imager acquires satisfactory image data. The adjustments may include flow rate adjustments, image acquisition data rate adjustments, and illumination adjustments. A processing unit in the channel may contain a laser or other component to destroy selected cells. A flared region in the channel may be used as a chromatograph.